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8e5t

Yeast co-transcriptional Noc1-Noc2 RNP assembly checkpoint intermediate

Method: ELECTRON MICROSCOPY Dmax: 237.7 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribosome biogenesis protein MAK21

OrganismNot specified

UniProt Q12176

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain 5； UniProt 1–1025 Not recorded NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9QJC Yeast pre-60S Domain II intermediate Deposited 2025-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain 5 1–1025（1025 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MAK21_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain 5； PDBConstruct 1–1025； UniProt 1–1025

NOC2 isoform 1

OrganismNot specified

UniProt A0A8H4BX61

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain 6； UniProt 1–710 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain 8 1–710（710 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NAD State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain 8 1–710（710 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A8H4BX61_YEASX
Isoform —
PDB entities 2
Chains and sequence ranges Author chain 6； PDBConstruct 1–710； UniProt 1–710

60S ribosomal protein L4-A

OrganismNot specified

UniProt P10664

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain C； UniProt 1–362 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L4 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L4 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain L4 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain L4 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V6I Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome Deposited 2010-10-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain BD 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain D 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 73-meric
Chain BD 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 355 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric
Chain DD 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 360 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain BC 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain DC 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain BC 2–362（361 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain BC 2–362（361 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain C 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain C 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain L4 2–362（361 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain l4 2–362（361 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain L4 2–362（361 aa）
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain L4 2–362（361 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain l4 2–362（361 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain l4 2–362（361 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain L4 2–362（361 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain G 1–362（362 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain C 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l4 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain C 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain H 1–362（362 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain H 1–362（362 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain H 1–362（362 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain H 1–362（362 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain H 1–362（362 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain C5 2–362（361 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain BE 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain l 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CF 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain l4 2–362（361 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain L4 2–362（361 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain L4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain l4 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain l 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain CF 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain F 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain F 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain l 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CF 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L4 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain l4 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain L4 2–362（361 aa）
Chain l4 2–362（361 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain G 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain C 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain C 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain C 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain C 2–362（361 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain C 2–362（361 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain C 2–362（361 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain G 1–362（362 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain l 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CF 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain BE 2–362（361 aa）
Chain YE 2–362（361 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain C 1–362（362 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain C 1–362（362 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain C 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain F 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain F 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain F 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain C 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain BE 2–362（361 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain D 1–362（362 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain D 1–362（362 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain D 1–362（362 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain G 2–362（361 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain G 2–362（361 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain G 2–362（361 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain D 1–362（362 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain D 1–362（362 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain D 1–362（362 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AF 2–362（361 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain j 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain BE 1–362（362 aa）
Chain YE 1–362（362 aa）
Chain ZE 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LC 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LC 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LC 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain Cy 1–362（362 aa）
Chain Fa 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain BE 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain BE 2–362（361 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain C 3–361（359 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain C 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LC 1–362（362 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LC 1–362（362 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain p 1–362（362 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LF 2–362（361 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain C 1–362（362 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain C 1–362（362 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AC 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AC 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AC 2–362（361 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LF 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LF 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain C 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain C 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain C 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHT Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 27-meric
Chain C 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OHY Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain C 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain C 1–362（362 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain C 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain C 1–362（362 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain C 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain C 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain C 1–362（362 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain BE 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain EC 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LG 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain l 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain l 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain l 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain l 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain l 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain l 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain LC 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain LC 2–362（361 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain BE 2–362（361 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain GG 1–362（362 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain GG 1–362（362 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain GG 1–362（362 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain GG 1–362（362 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain GG 1–362（362 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain GG 1–362（362 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain GG 1–362（362 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain GG 1–362（362 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain GG 1–362（362 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain GG 1–362（362 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain DO 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain LC 1–362（362 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain LC 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain l 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CF 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain l 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain CF 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LH 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LH 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LH 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain CF 1–362（362 aa）
Chain l 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LH 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain l 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain CF 1–362（362 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain LF 2–362（361 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LF 2–362（361 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain C 1–362（362 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain C 1–362（362 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain C 1–362（362 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain F 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain LC 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain F 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain F 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain F 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain F 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain LF 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain LF 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LF 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LF 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain LF 2–362（361 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AC 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AC 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain 3 1–362（362 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain Ly 1–362（362 aa）
Chain My 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric
Chain l 1–362（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AC 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9QJC Yeast pre-60S Domain II intermediate Deposited 2025-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain C 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LC 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LC 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

197 other PDB entries and 236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL4A_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–362； UniProt 1–362

Protein MAK16

OrganismNot specified

UniProt P10962

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain D； UniProt 1–306 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain Z 1–306（306 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain D 1–306（306 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain 3 1–306（306 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain 3 1–306（306 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain 3 1–306（306 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain 3 1–306（306 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain 3 1–306（306 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain 3 1–306（306 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain 3 1–306（306 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain R 1–306（306 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain R 1–306（306 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9QJC Yeast pre-60S Domain II intermediate Deposited 2025-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain D 1–306（306 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MAK16_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–306； UniProt 1–306

60S ribosomal protein L6-A

OrganismNot specified

UniProt Q02326

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain E； UniProt 1–176 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L6 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L6 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain L6 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain L6 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JBS eL6 protein from yeast 60S ribosomal subunit Deposited 2015-10-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer elution buffer (50 mM HEPES-KOH, 100 mM KOAc, 5 mM MgOAc, 1 mM EDTA, 2 mM DTT)；pH 6.8；elution buffer (50 mM HEPES-KOH, 100 mM KOAc, 5 mM MgOAc, 1 mM EDTA, 2 mM DTT)
cryo-EM vitrification conditions A 3 uL sample was applied onto a freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb for 30 seconds. The sample was then plunge-frozen in liquid ethane using a manual cryo-plunger in ambient atmosphere at 4 degrees C.；77 K；Cryogen ETHANE；A 3 uL sample was applied onto a freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb for 30 seconds. The sample was then plunge-frozen in liquid ethane using a manual cryo-plunger in ambient atmosphere at 4 degrees C.
Resolution 2.90 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V6I Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome Deposited 2010-10-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain BG 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain G 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 73-meric
Chain BF 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 355 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric
Chain DF 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 360 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain BE 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain DE 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain BE 2–176（175 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain BE 2–176（175 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain E 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain L6 2–176（175 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain l6 2–176（175 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain L6 2–176（175 aa）
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain L6 2–176（175 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain l6 2–176（175 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain l6 2–176（175 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain L6 2–176（175 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 2–176（175 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain I 1–176（176 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain E 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l6 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain E 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain J 1–176（176 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain J 1–176（176 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain J 1–176（176 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain J 1–176（176 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain J 1–176（176 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain l6 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain E5 2–176（175 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain BM 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain n 2–176（175 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CH 2–176（175 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain l6 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain l6 1–176（176 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain L6 1–176（176 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain l6 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L6 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain L6 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain l6 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain n 2–176（175 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain CH 2–176（175 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain H 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain H 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain n 2–176（175 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CH 2–176（175 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L6 2–176（175 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain l6 2–176（175 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain L6 2–176（175 aa）
Chain l6 2–176（175 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain I 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain E 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain E 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain E 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain E 2–176（175 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain E 2–176（175 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain E 2–176（175 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain I 1–176（176 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain n 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CH 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain BM 1–176（176 aa）
Chain YM 1–176（176 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain E 1–176（176 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain E 1–176（176 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain E 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain H 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain H 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain H 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain E 2–176（175 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain BM 2–176（175 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain G 1–176（176 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain G 1–176（176 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain G 1–176（176 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain I 2–176（175 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain I 2–176（175 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain I 2–176（175 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain G 1–176（176 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain G 1–176（176 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain G 1–176（176 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AH 2–176（175 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain BM 1–176（176 aa）
Chain YM 1–176（176 aa）
Chain ZM 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain Ey 1–176（176 aa）
Chain Ha 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain E 2–176（175 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XIQ Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6XIR Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 76-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain E 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LE 1–176（176 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LE 1–176（176 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain A 1–176（176 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain E 1–176（176 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain E 1–176（176 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AE 2–176（175 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AE 2–176（175 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain E 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain E 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain E 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHT Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 27-meric
Chain E 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OHY Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL06 1–176（176 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7TOP Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL06 1–176（176 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain E 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain E 1–176（176 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain E 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain E 1–176（176 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain E 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain E 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain E 1–176（176 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain BG 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain II 1–176（176 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain II 1–176（176 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain II 1–176（176 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain II 1–176（176 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain II 1–176（176 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain II 1–176（176 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain II 1–176（176 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain II 1–176（176 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain II 1–176（176 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain II 1–176（176 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8EUB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I Deposited 2022-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8EVP Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
8EVQ Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 241 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8EVR Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 217 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 W9C (1S,3S,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-alpha-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(propan-2-yl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EVS Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 254 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
8EVT Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) refined against a composite map Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 272 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8EWB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 242 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EWC Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure II Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 247 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain F8 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain LE 1–176（176 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain LE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain n 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CH 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain n 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain CH 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LJ 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LJ 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LJ 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain CH 1–176（176 aa）
Chain n 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LJ 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain n 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain CH 1–176（176 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8T2X Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 181 K POTASSIUM ION × 23 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8T2Y Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 197 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8T2Z Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POST Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AE 1–176（176 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8T30 Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AE 1–176（176 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8T3A Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, sordarin, and hibernating factor Los2 Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AE 1–176（176 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
8T3B Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AE 1–176（176 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8T3C Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AE 1–176（176 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
8T3D Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AE 1–176（176 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8T3E Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure IV Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AE 1–176（176 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8T3F Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AE 1–176（176 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain E 1–176（176 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain E 1–176（176 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain E 1–176（176 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain f 1–176（176 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain MA 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AE 1–176（176 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9QJC Yeast pre-60S Domain II intermediate Deposited 2025-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain E 1–176（176 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

182 other PDB entries and 221 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL6A_YEAST
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 1–176； UniProt 1–176

60S ribosomal protein L7-A

OrganismNot specified

UniProt P05737

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain F； UniProt 1–244 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L7 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L7 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain L7 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain L7 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V4B Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map. Deposited 2004-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain BF 82–243（162 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane
Resolution 11.70 Å
4V6I Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome Deposited 2010-10-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain Be 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain a 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 73-meric
Chain BG 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 355 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric
Chain DG 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 360 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain BF 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain DF 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain BF 2–244（243 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain BF 2–244（243 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain F 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain F 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain L7 2–244（243 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain l7 2–244（243 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain L7 2–244（243 aa）
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain L7 2–244（243 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain l7 2–244（243 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain l7 2–244（243 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain L7 2–244（243 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 2–244（243 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain l7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 2–244（243 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain J 1–244（244 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain F 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 22–244（223 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l7 22–244（223 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain F 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain K 1–244（244 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain K 1–244（244 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain K 1–244（244 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain K 1–244（244 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain K 1–244（244 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L7 22–244（223 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain l7 22–244（223 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain F5 23–244（222 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain BO 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain o 23–244（222 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CI 23–244（222 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 22–244（223 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain l7 22–244（223 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain l7 19–244（226 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain L7 19–244（226 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain l7 22–244（223 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L7 22–244（223 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain L7 22–244（223 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain l7 22–244（223 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain o 23–244（222 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain CI 23–244（222 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain I 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain I 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain o 23–244（222 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CI 23–244（222 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L7 22–244（223 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain l7 22–244（223 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain L7 22–244（223 aa）
Chain l7 22–244（223 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain J 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain F 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain F 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain F 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain F 23–244（222 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain F 23–244（222 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain F 23–244（222 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain J 1–244（244 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain o 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CI 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain BO 22–244（223 aa）
Chain YO 22–244（223 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain F 1–244（244 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain F 1–244（244 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain F 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain I 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain I 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain I 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain F 23–244（222 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain BO 23–244（222 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain b 1–244（244 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain b 1–244（244 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain b 1–244（244 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain J 23–244（222 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain J 23–244（222 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain J 23–244（222 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain b 1–244（244 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain b 1–244（244 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain b 1–244（244 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AI 2–244（243 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain m 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain BO 1–244（244 aa）
Chain YO 1–244（244 aa）
Chain ZO 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LF 23–244（222 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LF 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LF 23–244（222 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain Fy 1–244（244 aa）
Chain Ia 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain BO 23–244（222 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain BO 23–244（222 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain F 23–244（222 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XIQ Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6XIR Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 76-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain F 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LF 1–244（244 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LF 1–244（244 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain C 1–244（244 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LI 23–244（222 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain F 1–244（244 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain F 1–244（244 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AF 23–244（222 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AF 23–244（222 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AF 23–244（222 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LI 23–244（222 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LI 23–244（222 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain F 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain F 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain F 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHT Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 27-meric
Chain F 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OHY Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OSA Pre-translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands Deposited 2021-06-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain uL30 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 490 ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG10K, KSCN, TRIS-HAC
Resolution 3.00 Å R-free 0.250
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL07 1–244（244 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7TOP Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL07 1–244（244 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain F 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain F 1–244（244 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain F 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain F 1–244（244 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain F 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain F 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain F 1–244（244 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZPQ Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) Deposited 2022-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BF 23–244（222 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7ZRS Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map Deposited 2022-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BF 23–244（222 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain BH 23–244（222 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUW Structure of RQT (C1) bound to the stalled ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BF 23–244（222 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain EF 23–244（222 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LJ 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain o 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain o 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGU Yeast RQC complex in state E Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain o 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain o 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain o 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain o 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain o 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain LF 23–244（222 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain LF 23–244（222 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8BN3 Yeast 80S, ES7s delta, eIF5A, Stm1 containing Deposited 2022-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain L7 23–244（222 aa）
Not recorded MG MAGNESIUM ION × 220 K POTASSIUM ION × 72 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 SPD SPERMIDINE × 3 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.40 Å
8BQD Yeast 80S ribosome in complex with Map1 (conformation 1) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain BO 23–244（222 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain BO 23–244（222 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain JJ 1–244（244 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain JJ 1–244（244 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain JJ 1–244（244 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain JJ 1–244（244 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain JJ 1–244（244 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain JJ 1–244（244 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain JJ 1–244（244 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain JJ 1–244（244 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain JJ 1–244（244 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain JJ 1–244（244 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8EUB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I Deposited 2022-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8EVP Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
8EVQ Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 241 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8EVR Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 217 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 W9C (1S,3S,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-alpha-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(propan-2-yl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EVS Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 254 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
8EVT Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) refined against a composite map Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 272 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8EWB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 242 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EWC Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure II Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 247 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain Gu 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain LF 1–244（244 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain LF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain o 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CI 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain o 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain CI 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LK 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LK 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LK 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain CI 1–244（244 aa）
Chain o 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LK 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain o 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain CI 1–244（244 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8T2X Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 181 K POTASSIUM ION × 23 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8T2Y Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 197 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8T2Z Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POST Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AF 1–244（244 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8T30 Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AF 1–244（244 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8T3A Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, sordarin, and hibernating factor Los2 Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AF 1–244（244 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
8T3B Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AF 1–244（244 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8T3C Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AF 1–244（244 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
8T3D Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AF 1–244（244 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8T3E Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure IV Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AF 1–244（244 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8T3F Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AF 1–244（244 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain LI 23–244（222 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LI 23–244（222 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain F 1–244（244 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain F 1–244（244 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain F 1–244（244 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain I 23–244（222 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain LF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain I 22–244（223 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain I 22–244（223 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain I 22–244（223 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain I 22–244（223 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain LI 23–244（222 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain LI 23–244（222 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LI 23–244（222 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LI 23–244（222 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain LI 23–244（222 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain g 1–244（244 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain LB 1–244（244 aa）
Chain MB 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric
Chain o 1–244（244 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AF 1–244（244 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9QJC Yeast pre-60S Domain II intermediate Deposited 2025-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain F 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LF 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LF 1–244（244 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

227 other PDB entries and 266 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL7A_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain F； PDBConstruct 1–244； UniProt 1–244

60S ribosomal protein L8-A

OrganismNot specified

UniProt P17076

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain G； UniProt 1–256 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L8 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L8 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain L8 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain L8 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V4B Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map. Deposited 2004-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain BG 101–219（119 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane
Resolution 11.70 Å
4V6I Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome Deposited 2010-10-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain BH 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain H 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 73-meric
Chain BH 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 355 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric
Chain DH 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 360 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain BG 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain DG 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain BG 2–256（255 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain BG 2–256（255 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain G 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain G 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain L8 2–256（255 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain l8 2–256（255 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain L8 2–256（255 aa）
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain L8 2–256（255 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain l8 2–256（255 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 2–256（255 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain l8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 2–256（255 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain K 1–256（256 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain G 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 24–256（233 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain l8 24–254（231 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain G 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain L 1–256（256 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain L 1–256（256 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain L 1–256（256 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain L 1–256（256 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain L 1–256（256 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L8 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain l8 24–248（225 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain G5 24–256（233 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain AA 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain p 24–256（233 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CJ 24–256（233 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain l8 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain l8 24–254（231 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain L8 24–254（231 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain l8 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain L8 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain L8 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain l8 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain p 24–256（233 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain CJ 24–256（233 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain J 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain J 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain p 24–256（233 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CJ 24–256（233 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain L8 24–256（233 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain l8 24–256（233 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain L8 24–256（233 aa）
Chain l8 24–248（225 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain K 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6CB1 Yeast nucleolar pre-60S ribosomal subunit (state 3) Deposited 2018-02-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 37 PDB declaration: 40-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain G 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain G 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain G 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain G 24–256（233 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain G 24–256（233 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain G 24–256（233 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain K 1–256（256 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain p 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CJ 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain AA 24–254（231 aa）
Chain XA 24–254（231 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain G 1–256（256 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain G 1–256（256 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain G 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain J 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain J 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain J 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain G 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain AA 24–256（233 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain H 1–256（256 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain H 1–256（256 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain H 1–256（256 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain K 24–256（233 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain K 24–256（233 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain K 24–256（233 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain H 1–256（256 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain H 1–256（256 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain H 1–256（256 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AJ 24–256（233 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain n 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain AA 1–256（256 aa）
Chain XA 1–256（256 aa）
Chain zA 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LG 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LG 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LG 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain Gy 1–256（256 aa）
Chain Ja 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain AA 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AA 24–256（233 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain G 24–256（233 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain G 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LG 1–256（256 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LG 1–256（256 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain b 1–256（256 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LJ 24–256（233 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain G 1–256（256 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain G 1–256（256 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AG 24–253（230 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AG 24–253（230 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AG 24–253（230 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LJ 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LJ 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain G 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain G 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain G 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OHY Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OSA Pre-translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands Deposited 2021-06-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain eL8 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 490 ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG10K, KSCN, TRIS-HAC
Resolution 3.00 Å R-free 0.250
7OSM Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands Deposited 2021-06-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain eL8 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 499 ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 6000, KSCN, Tris-HAc
Resolution 3.00 Å R-free 0.284
7R6K State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region Deposited 2021-06-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 15 PDB declaration: hexadecameric
Chain G 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
7R6Q State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model Deposited 2021-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain G 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
7R72 State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 local model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7RR5 Structure of ribosomal complex bound with Rbg1/Tma46 Deposited 2021-08-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain LG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 286 ASP ASPARTIC ACID × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL08 1–256（256 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7TOP Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL08 1–256（256 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain G 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain G 1–256（256 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain G 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain G 1–256（256 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain G 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain G 1–256（256 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZPQ Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) Deposited 2022-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BG 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7ZRS Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map Deposited 2022-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BG 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain BI 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain EG 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LK 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain p 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain p 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGU Yeast RQC complex in state E Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain p 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain p 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain p 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain p 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain p 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain LG 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain LG 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8BN3 Yeast 80S, ES7s delta, eIF5A, Stm1 containing Deposited 2022-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain L8 24–256（233 aa）
Not recorded MG MAGNESIUM ION × 220 K POTASSIUM ION × 72 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 SPD SPERMIDINE × 3 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.40 Å
8BQD Yeast 80S ribosome in complex with Map1 (conformation 1) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AA 24–256（233 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AA 24–256（233 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain KK 1–256（256 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain KK 1–256（256 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain KK 1–256（256 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain KK 1–256（256 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain KK 1–256（256 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain KK 1–256（256 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain KK 1–256（256 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain KK 1–256（256 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain KK 1–256（256 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain KK 1–256（256 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8EUB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I Deposited 2022-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8EVP Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
8EVQ Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 241 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8EVR Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 217 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 W9C (1S,3S,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-alpha-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(propan-2-yl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EVS Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 254 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
8EVT Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) refined against a composite map Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 272 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8EWB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 242 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EWC Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure II Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 247 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain Hj 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain LG 1–256（256 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain LG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain p 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CJ 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain p 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain CJ 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LL 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LL 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LL 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain CJ 1–256（256 aa）
Chain p 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain LL 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain p 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain CJ 1–256（256 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8T2X Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 181 K POTASSIUM ION × 23 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8T2Y Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 197 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8T2Z Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POST Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AG 1–256（256 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8T30 Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AG 1–256（256 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8T3A Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, sordarin, and hibernating factor Los2 Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AG 1–256（256 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
8T3B Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AG 1–256（256 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8T3C Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AG 1–256（256 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
8T3D Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AG 1–256（256 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8T3E Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure IV Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AG 1–256（256 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8T3F Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AG 1–256（256 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain G 1–256（256 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain G 1–256（256 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain G 1–256（256 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain J 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain LG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain J 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain J 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain J 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain J 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain LJ 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain LJ 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LJ 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LJ 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain LJ 24–256（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain h 1–256（256 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain LC 1–256（256 aa）
Chain MC 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric
Chain p 1–256（256 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AG 1–256（256 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LG 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LG 1–256（256 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

224 other PDB entries and 262 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL8A_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain G； PDBConstruct 1–256； UniProt 1–256

Proteasome-interacting protein CIC1

OrganismNot specified

UniProt P38779

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain K； UniProt 1–376 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain H 1–376（376 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain K 1–376（376 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain K 1–376（376 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain K 1–376（376 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain K 1–376（376 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain K 1–376（376 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain K 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7R6Q State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model Deposited 2021-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain K 1–376（376 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain K 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain K 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain K 1–376（376 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain K 1–339（339 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain K 1–376（376 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain K 1–376（376 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain K 1–376（376 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain K 1–376（376 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å

30 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CIC1_YEAST
Isoform —
PDB entities 8
Chains and sequence ranges Author chain K； PDBConstruct 1–376； UniProt 1–376

60S ribosomal protein L13-A

OrganismNot specified

UniProt Q12690

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain L； UniProt 1–199 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 53 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 53 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain 63 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 63 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain K 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain BL 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain DL 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain BL 2–199（198 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain BL 2–199（198 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain L 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain L 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain M3 2–199（198 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain m3 2–199（198 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain M3 2–199（198 aa）
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain M3 2–199（198 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain m3 2–199（198 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain m3 2–199（198 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain M3 2–199（198 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–199（198 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain m3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain N 1–199（199 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain L 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–195（194 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m3 2–195（194 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain L 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain Q 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain Q 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain Q 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain Q 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain Q 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M3 2–195（194 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m3 2–195（194 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain L5 2–194（193 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain AJ 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain t 2–194（193 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CN 2–194（193 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–195（194 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain m3 2–195（194 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain m3 2–195（194 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain M3 2–195（194 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain m3 2–195（194 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M3 2–195（194 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M3 2–195（194 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain m3 2–195（194 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain t 2–194（193 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain CN 2–194（193 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain N 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain N 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain t 2–194（193 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CN 2–194（193 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M3 2–195（194 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m3 2–195（194 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain M3 2–195（194 aa）
Chain m3 2–195（194 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain P 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain L 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain L 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain L 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain L 2–194（193 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain L 2–194（193 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain L 2–194（193 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain N 1–199（199 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain t 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CN 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain AJ 2–195（194 aa）
Chain XJ 2–195（194 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain L 1–199（199 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain L 1–199（199 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain L 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain N 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain N 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain N 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain L 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain AJ 2–194（193 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain K 1–199（199 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain K 1–199（199 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain K 1–199（199 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain N 2–194（193 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain N 2–194（193 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain N 2–194（193 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain K 1–199（199 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain K 1–199（199 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain K 1–199（199 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AN 2–199（198 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain r 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain AJ 1–199（199 aa）
Chain XJ 1–199（199 aa）
Chain zJ 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LL 2–194（193 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LL 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LL 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain Ly 1–199（199 aa）
Chain Na 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain AJ 2–194（193 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AJ 2–194（193 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain L 2–199（198 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XIQ Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6XIR Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 76-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain L 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LL 1–199（199 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LL 1–199（199 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain k 1–199（199 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LN 2–194（193 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain L 1–199（199 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain L 1–199（199 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AL 2–194（193 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AL 2–194（193 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AL 2–194（193 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LN 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LN 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain L 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain L 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain L 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OHY Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7R6Q State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model Deposited 2021-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain L 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL13 1–199（199 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7TOP Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL13 1–199（199 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain L 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain L 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain L 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain L 1–199（199 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain L 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain L 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain L 1–199（199 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZPQ Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) Deposited 2022-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BK 2–194（193 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7ZRS Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map Deposited 2022-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BK 2–194（193 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain BM 2–194（193 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUW Structure of RQT (C1) bound to the stalled ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BK 2–194（193 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain EK 2–194（193 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain t 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain t 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGU Yeast RQC complex in state E Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain t 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain t 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain t 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain t 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain t 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain LL 2–194（193 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain LL 2–194（193 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8BN3 Yeast 80S, ES7s delta, eIF5A, Stm1 containing Deposited 2022-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain M3 2–194（193 aa）
Not recorded MG MAGNESIUM ION × 220 K POTASSIUM ION × 72 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 SPD SPERMIDINE × 3 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.40 Å
8BQD Yeast 80S ribosome in complex with Map1 (conformation 1) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AJ 2–194（193 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AJ 2–194（193 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain OO 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain OO 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain OO 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain OO 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain OO 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain OO 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain OO 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain OO 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain OO 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain OO 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8EUB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I Deposited 2022-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8EVP Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
8EVQ Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 241 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8EVR Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 217 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 W9C (1S,3S,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-alpha-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(propan-2-yl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EVS Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 254 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
8EVT Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) refined against a composite map Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 272 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8EWB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 242 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EWC Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure II Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 247 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain LL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain LL 1–199（199 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain LL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain t 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CN 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain t 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain CN 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JT 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JT 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JT 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain CN 1–199（199 aa）
Chain t 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JT 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain t 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain CN 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8T2X Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 181 K POTASSIUM ION × 23 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8T2Y Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 197 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8T2Z Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POST Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AL 1–199（199 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8T30 Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AL 1–199（199 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8T3A Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, sordarin, and hibernating factor Los2 Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AL 1–199（199 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
8T3B Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AL 1–199（199 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8T3C Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AL 1–199（199 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
8T3D Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AL 1–199（199 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8T3E Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure IV Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AL 1–199（199 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8T3F Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AL 1–199（199 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain LN 2–194（193 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LN 2–194（193 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain L 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain L 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain L 1–199（199 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain N 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain LL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain N 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain N 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain N 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain N 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain LN 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain LN 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LN 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LN 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain LN 2–194（193 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain m 1–199（199 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain LG 1–199（199 aa）
Chain MG 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric
Chain t 1–199（199 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AL 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LL 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LL 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

222 other PDB entries and 260 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL13A_YEAST
Isoform —
PDB entities 9
Chains and sequence ranges Author chain L； PDBConstruct 1–199； UniProt 1–199

60S ribosomal protein L14-A

OrganismNot specified

UniProt P36105

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain M； UniProt 1–138 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 54 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 54 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain 64 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 64 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain M 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 73-meric
Chain BN 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 355 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric
Chain DN 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 360 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain BM 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain DM 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain M 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain M 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain M4 2–138（137 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain m4 2–138（137 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain M4 2–138（137 aa）
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain M4 2–138（137 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain m4 2–138（137 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain m4 2–138（137 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain M4 2–138（137 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain O 1–138（138 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain M 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m4 2–138（137 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain M 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain R 1–138（138 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain R 1–138（138 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain R 1–138（138 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain R 1–138（138 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain R 1–138（138 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain M5 3–138（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain AM 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain u 3–138（136 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CO 3–138（136 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain m4 2–138（137 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain M4 2–138（137 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain m4 2–138（137 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain u 3–138（136 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain CO 3–138（136 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain O 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain O 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain u 3–138（136 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CO 3–138（136 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M4 2–138（137 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m4 2–138（137 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain M4 2–138（137 aa）
Chain m4 2–138（137 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain Q 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6CB1 Yeast nucleolar pre-60S ribosomal subunit (state 3) Deposited 2018-02-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 37 PDB declaration: 40-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain M 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain M 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain M 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain M 3–138（136 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain M 3–138（136 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain M 3–138（136 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain O 1–138（138 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain u 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CO 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain AM 2–138（137 aa）
Chain XM 2–138（137 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain M 1–138（138 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain M 1–138（138 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain M 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain O 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain O 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain O 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain M 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain AM 3–138（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain O 3–138（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain O 3–138（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain O 3–138（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AO 2–138（137 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain s 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain AM 1–138（138 aa）
Chain XM 1–138（138 aa）
Chain zM 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LM 3–138（136 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LM 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LM 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain My 1–138（138 aa）
Chain Oa 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain AM 3–138（136 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AM 3–138（136 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain M 2–137（136 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XIQ Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6XIR Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 76-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain M 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LM 1–138（138 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LM 1–138（138 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain N 1–138（138 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LO 3–138（136 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain M 1–138（138 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain M 1–138（138 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AM 3–138（136 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AM 3–138（136 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AM 3–138（136 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LO 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LO 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain M 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain M 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain M 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHT Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 27-meric
Chain M 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OHY Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OSA Pre-translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands Deposited 2021-06-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain eL14 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 490 ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG10K, KSCN, TRIS-HAC
Resolution 3.00 Å R-free 0.250
7OSM Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands Deposited 2021-06-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain eL14 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 499 ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 6000, KSCN, Tris-HAc
Resolution 3.00 Å R-free 0.284
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7RR5 Structure of ribosomal complex bound with Rbg1/Tma46 Deposited 2021-08-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain LM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 286 ASP ASPARTIC ACID × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL14 1–138（138 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7TOP Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL14 1–138（138 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain M 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain M 1–138（138 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain M 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain M 1–138（138 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain M 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain M 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain M 1–138（138 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZPQ Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) Deposited 2022-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BL 3–138（136 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7ZRS Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map Deposited 2022-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BL 3–138（136 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain BN 3–138（136 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUW Structure of RQT (C1) bound to the stalled ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BL 3–138（136 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain EL 3–138（136 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LP 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain u 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain u 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGU Yeast RQC complex in state E Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain u 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain u 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain u 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain u 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain u 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain LM 3–138（136 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain LM 3–138（136 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8BN3 Yeast 80S, ES7s delta, eIF5A, Stm1 containing Deposited 2022-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain M4 3–138（136 aa）
Not recorded MG MAGNESIUM ION × 220 K POTASSIUM ION × 72 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 SPD SPERMIDINE × 3 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.40 Å
8BQD Yeast 80S ribosome in complex with Map1 (conformation 1) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AM 3–138（136 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AM 3–138（136 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain PP 1–138（138 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain PP 1–138（138 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain PP 1–138（138 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain PP 1–138（138 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain PP 1–138（138 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain PP 1–138（138 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain PP 1–138（138 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain PP 1–138（138 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain PP 1–138（138 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain PP 1–138（138 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8EUB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I Deposited 2022-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8EVP Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
8EVQ Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 241 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8EVR Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 217 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 W9C (1S,3S,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-alpha-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(propan-2-yl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EVS Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 254 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
8EVT Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) refined against a composite map Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 272 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8EWB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 242 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EWC Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure II Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 247 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain MQ 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain LM 1–138（138 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain LM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain u 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CO 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain u 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain CO 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JU 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JU 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JU 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain CO 1–138（138 aa）
Chain u 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JU 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain u 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain CO 1–138（138 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8T2X Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 181 K POTASSIUM ION × 23 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8T2Y Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 197 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8T2Z Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POST Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AM 1–138（138 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8T30 Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AM 1–138（138 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8T3A Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, sordarin, and hibernating factor Los2 Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AM 1–138（138 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
8T3B Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AM 1–138（138 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8T3C Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AM 1–138（138 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
8T3D Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AM 1–138（138 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8T3E Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure IV Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AM 1–138（138 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8T3F Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AM 1–138（138 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain LO 3–138（136 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LO 3–138（136 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain M 1–138（138 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain M 1–138（138 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain M 1–138（138 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain O 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain LM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain O 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain O 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain O 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain O 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain LO 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain LO 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LO 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LO 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain LO 3–138（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain n 1–138（138 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain LH 1–138（138 aa）
Chain MH 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric
Chain u 1–138（138 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AM 1–138（138 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9QJC Yeast pre-60S Domain II intermediate Deposited 2025-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain M 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LM 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LM 1–138（138 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

226 other PDB entries and 265 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL14A_YEAST
Isoform —
PDB entities 10
Chains and sequence ranges Author chain M； PDBConstruct 1–138； UniProt 1–138

60S ribosomal protein L15-A

OrganismNot specified

UniProt P05748

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain N； UniProt 1–204 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 55 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 55 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain 65 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 65 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V4B Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map. Deposited 2004-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain BL 1–203（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane
Resolution 11.70 Å
4V6I Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome Deposited 2010-10-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain BP 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain O 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 73-meric
Chain BO 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 355 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric
Chain DO 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 360 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain BN 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain DN 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain BN 2–204（203 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain BN 2–204（203 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain N 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain N 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain M5 2–204（203 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain m5 2–204（203 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain M5 2–204（203 aa）
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain M5 2–204（203 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain m5 2–204（203 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain m5 2–204（203 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain M5 2–204（203 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain P 1–204（204 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain N 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m5 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain N 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain S 1–204（204 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain S 1–204（204 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain S 1–204（204 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain S 1–204（204 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain S 1–204（204 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain N5 2–204（203 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain AQ 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain v 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CP 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain m5 2–204（203 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain M5 2–204（203 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain m5 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain v 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain CP 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain a 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain a 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain v 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CP 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M5 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m5 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain M5 2–204（203 aa）
Chain m5 2–204（203 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain R 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6CB1 Yeast nucleolar pre-60S ribosomal subunit (state 3) Deposited 2018-02-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 37 PDB declaration: 40-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain N 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain N 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain N 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain N 2–204（203 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain N 2–204（203 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain N 2–204（203 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain P 1–204（204 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain v 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CP 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain AQ 2–204（203 aa）
Chain XQ 2–204（203 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain N 1–204（204 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain N 1–204（204 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain N 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain a 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain a 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain a 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain N 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain AQ 2–204（203 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain O 1–204（204 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain O 1–204（204 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain O 1–204（204 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain p 2–204（203 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain p 2–204（203 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain p 2–204（203 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain O 1–204（204 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain O 1–204（204 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain O 1–204（204 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AP 2–204（203 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain t 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain AQ 1–204（204 aa）
Chain XQ 1–204（204 aa）
Chain zQ 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LN 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LN 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LN 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain Ny 1–204（204 aa）
Chain Pa 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain AQ 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AQ 2–204（203 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain N 2–203（202 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XIQ Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6XIR Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 76-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain N 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LN 1–204（204 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LN 1–204（204 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain R 1–204（204 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LP 2–204（203 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain N 1–204（204 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain N 1–204（204 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AN 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AN 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AN 2–204（203 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LP 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LP 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain N 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain N 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain N 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OHY Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OSA Pre-translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands Deposited 2021-06-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain eL15 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 490 ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG10K, KSCN, TRIS-HAC
Resolution 3.00 Å R-free 0.250
7OSM Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands Deposited 2021-06-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain eL15 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 499 ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 6000, KSCN, Tris-HAc
Resolution 3.00 Å R-free 0.284
7R6K State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region Deposited 2021-06-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 15 PDB declaration: hexadecameric
Chain N 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
7R6Q State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model Deposited 2021-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain N 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7RR5 Structure of ribosomal complex bound with Rbg1/Tma46 Deposited 2021-08-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain LN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 286 ASP ASPARTIC ACID × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL15 1–204（204 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7TOP Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL15 1–204（204 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain N 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain N 1–204（204 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain N 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain N 1–204（204 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain N 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain N 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain N 1–204（204 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZPQ Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) Deposited 2022-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BM 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7ZRS Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map Deposited 2022-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BM 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain BO 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain EM 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LQ 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain A 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain A 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGU Yeast RQC complex in state E Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain A 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain A 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain A 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain A 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain A 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain LN 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain LN 2–204（203 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8BQD Yeast 80S ribosome in complex with Map1 (conformation 1) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AQ 2–204（203 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AQ 2–204（203 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain QQ 1–204（204 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain QQ 1–204（204 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain QQ 1–204（204 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain QQ 1–204（204 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain QQ 1–204（204 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain QQ 1–204（204 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain QQ 1–204（204 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain QQ 1–204（204 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain QQ 1–204（204 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain QQ 1–204（204 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8EUB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I Deposited 2022-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8EVP Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
8EVQ Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 241 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8EVR Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 217 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 W9C (1S,3S,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-alpha-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(propan-2-yl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EVS Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 254 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
8EVT Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) refined against a composite map Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 272 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8EWB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 242 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EWC Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure II Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 247 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain No 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain LN 1–204（204 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain LN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain v 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CP 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain v 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain CP 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JV 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JV 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JV 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain CP 1–204（204 aa）
Chain v 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JV 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain v 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain CP 1–204（204 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8T2X Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 181 K POTASSIUM ION × 23 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8T2Y Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 197 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8T2Z Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POST Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AN 1–204（204 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8T30 Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AN 1–204（204 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8T3A Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, sordarin, and hibernating factor Los2 Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AN 1–204（204 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
8T3B Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AN 1–204（204 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8T3C Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AN 1–204（204 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
8T3D Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AN 1–204（204 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8T3E Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure IV Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AN 1–204（204 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8T3F Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AN 1–204（204 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain LP 2–204（203 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LP 2–204（203 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain N 1–204（204 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain N 1–204（204 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain N 1–204（204 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain P 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain LN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain P 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain P 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain P 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain P 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain LP 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain LP 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LP 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LP 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain LP 2–204（203 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain o 1–204（204 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain LI 1–204（204 aa）
Chain MI 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AN 1–204（204 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LN 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LN 1–204（204 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

227 other PDB entries and 266 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL15A_YEAST
Isoform —
PDB entities 11
Chains and sequence ranges Author chain N； PDBConstruct 1–204； UniProt 1–204

60S ribosomal protein L18-A

OrganismNot specified

UniProt P0CX49

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain Q； UniProt 1–186 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 58 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 58 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain 68 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 68 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Q 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain BQ 1–186（186 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain DQ 1–186（186 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain BQ 2–186（185 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain BQ 2–186（185 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain Q 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain Q 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain M8 2–186（185 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain m8 2–186（185 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain M8 2–186（185 aa）
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain M8 2–186（185 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain m8 2–186（185 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain m8 2–186（185 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain M8 2–186（185 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain S 1–186（186 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain Q 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m8 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Q 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain V 1–186（186 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain V 1–186（186 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain V 1–186（186 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain V 1–186（186 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain V 1–186（186 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Q5 2–186（185 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain BB 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain y 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CS 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain m8 2–186（185 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain M8 2–186（185 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain m8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain y 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain CS 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain d 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain d 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain y 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CS 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M8 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m8 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain M8 2–186（185 aa）
Chain m8 2–186（185 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain U 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain Q 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain Q 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain Q 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain Q 2–186（185 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Q 2–186（185 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Q 2–186（185 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain S 1–186（186 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain y 1–186（186 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CS 1–186（186 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain BB 2–186（185 aa）
Chain YB 2–186（185 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain Q 1–186（186 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Q 1–186（186 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Q 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain d 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain d 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain d 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Q 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain BB 2–186（185 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain S 2–186（185 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain S 2–186（185 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain S 2–186（185 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AS 2–186（185 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain w 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain BB 1–186（186 aa）
Chain YB 1–186（186 aa）
Chain ZB 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LQ 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LQ 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LQ 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain B 1–186（186 aa）
Chain Qy 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain BB 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain BB 2–186（185 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Q 3–186（184 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XIQ Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6XIR Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 76-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain Q 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LQ 1–186（186 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LQ 1–186（186 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain m 1–186（186 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lm 2–186（185 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain Q 1–186（186 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain Q 1–186（186 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AQ 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AQ 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AQ 2–186（185 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LS 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LS 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain Q 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain Q 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain Q 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHT Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 27-meric
Chain Q 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OHY Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL18 1–186（186 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7TOP Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL18 1–186（186 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain Q 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain Q 1–186（186 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain Q 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain Q 1–186（186 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain Q 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain Q 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain Q 1–186（186 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZPQ Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) Deposited 2022-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BP 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7ZRS Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map Deposited 2022-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BP 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain BR 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUW Structure of RQT (C1) bound to the stalled ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BP 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain EP 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LT 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain D 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain D 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGU Yeast RQC complex in state E Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain D 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain D 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain D 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain D 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain D 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain LQ 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain LQ 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8BN3 Yeast 80S, ES7s delta, eIF5A, Stm1 containing Deposited 2022-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain M8 2–186（185 aa）
Not recorded MG MAGNESIUM ION × 220 K POTASSIUM ION × 72 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 SPD SPERMIDINE × 3 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.40 Å
8BQD Yeast 80S ribosome in complex with Map1 (conformation 1) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain BB 2–186（185 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain BB 2–186（185 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain C 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain C 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain C 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain C 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain C 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain C 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain C 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain C 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain C 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain C 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8EUB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I Deposited 2022-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8EVP Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
8EVQ Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 241 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8EVR Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 217 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 W9C (1S,3S,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-alpha-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(propan-2-yl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EVS Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 254 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
8EVT Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) refined against a composite map Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 272 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8EWB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 242 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EWC Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure II Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 247 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain Qk 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain LQ 1–186（186 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain LQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain y 1–186（186 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CS 1–186（186 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain y 1–186（186 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain CS 1–186（186 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain QP 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain QP 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain QP 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain CS 1–186（186 aa）
Chain y 1–186（186 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain QP 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain y 1–186（186 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain CS 1–186（186 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8T2X Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 181 K POTASSIUM ION × 23 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8T2Y Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 197 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8T2Z Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POST Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AQ 1–186（186 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8T30 Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AQ 1–186（186 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8T3A Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, sordarin, and hibernating factor Los2 Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AQ 1–186（186 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
8T3B Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AQ 1–186（186 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8T3C Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AQ 1–186（186 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
8T3D Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AQ 1–186（186 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8T3E Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure IV Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AQ 1–186（186 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8T3F Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AQ 1–186（186 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain LS 2–186（185 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LS 2–186（185 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Q 1–186（186 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain Q 1–186（186 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain Q 1–186（186 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain S 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain LQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain S 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain S 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain S 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain S 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain LS 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain LS 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LS 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LS 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain LS 2–186（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain r 1–186（186 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain LL 1–186（186 aa）
Chain ML 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric
Chain 4 1–186（186 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AQ 1–186（186 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9QJC Yeast pre-60S Domain II intermediate Deposited 2025-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain Q 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LQ 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LQ 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

223 other PDB entries and 261 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL18A_YEAST
Isoform —
PDB entities 12
Chains and sequence ranges Author chain Q； PDBConstruct 1–186； UniProt 1–186

60S ribosomal protein L20-A

OrganismNot specified

UniProt P0CX23

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain S； UniProt 1–172 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 60 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 60 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain 70 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 70 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain S 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain BS 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain DS 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain S 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain S 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain N0 1–172（172 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain n0 1–172（172 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain N0 1–172（172 aa）
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain N0 1–172（172 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain n0 1–172（172 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain n0 1–172（172 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain N0 1–172（172 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain U 1–172（172 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain S 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain n0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain S 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain X 1–172（172 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain X 1–172（172 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain X 1–172（172 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain X 1–172（172 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain X 1–172（172 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain S5 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain BH 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain 0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CU 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain n0 1–172（172 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain N0 1–172（172 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain n0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain 0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain CU 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain f 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain f 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain 0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CU 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain N0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain n0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain N0 1–172（172 aa）
Chain n0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain W 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain S 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain S 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain S 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain U 1–172（172 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain 0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CU 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain BH 1–172（172 aa）
Chain YH 1–172（172 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain S 1–172（172 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain S 1–172（172 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain S 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain f 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain f 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain f 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain S 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain BH 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain U 1–172（172 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain U 1–172（172 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain U 1–172（172 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AU 1–172（172 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain y 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain BH 1–172（172 aa）
Chain YH 1–172（172 aa）
Chain ZH 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LS 2–172（171 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LS 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LS 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain D 1–172（172 aa）
Chain Sy 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain BH 2–172（171 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain BH 2–172（171 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain S 4–172（169 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XIQ Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6XIR Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 76-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain S 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LS 1–172（172 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LS 1–172（172 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain s 1–172（172 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lo 2–172（171 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain S 1–172（172 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain S 1–172（172 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AS 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AS 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AS 1–172（172 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LU 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LU 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain S 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain S 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain S 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHT Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 27-meric
Chain S 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OHY Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7RR5 Structure of ribosomal complex bound with Rbg1/Tma46 Deposited 2021-08-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain LS 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 286 ASP ASPARTIC ACID × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL20 1–172（172 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7TOP Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL20 1–172（172 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain S 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain S 1–172（172 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain S 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain S 1–172（172 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain S 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain S 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain S 1–172（172 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZPQ Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) Deposited 2022-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BR 2–172（171 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7ZRS Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map Deposited 2022-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BR 2–172（171 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain BT 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUW Structure of RQT (C1) bound to the stalled ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BR 2–172（171 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain ER 2–172（171 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LV 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain F 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain F 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGU Yeast RQC complex in state E Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain F 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain F 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain F 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain F 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain F 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain LS 2–172（171 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain LS 2–172（171 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8BN3 Yeast 80S, ES7s delta, eIF5A, Stm1 containing Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain N0 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 220 K POTASSIUM ION × 72 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 SPD SPERMIDINE × 3 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.40 Å
8BQD Yeast 80S ribosome in complex with Map1 (conformation 1) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain BH 2–172（171 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain BH 2–172（171 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain E 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain E 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain E 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain E 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain E 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain E 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain E 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain E 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain E 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain E 1–172（172 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain SZ 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain LS 1–172（172 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain LS 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain 0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CU 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain 0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain CU 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain QS 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain QS 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain QS 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain 0 1–172（172 aa）
Chain CU 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain QS 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain 0 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain CU 1–172（172 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain LU 2–172（171 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LU 2–172（171 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain S 1–172（172 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain S 1–172（172 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain S 1–172（172 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain U 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain LS 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain U 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain U 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain U 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain U 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain LU 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain LU 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LU 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LU 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain LU 2–172（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain t 1–172（172 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain LN 1–172（172 aa）
Chain MN 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric
Chain 6 1–172（172 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AS 1–172（172 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9QJC Yeast pre-60S Domain II intermediate Deposited 2025-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain S 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LS 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LS 1–172（172 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

202 other PDB entries and 240 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL20A_YEAST
Isoform —
PDB entities 13
Chains and sequence ranges Author chain S； PDBConstruct 1–172； UniProt 1–172

Ribosome biogenesis protein BRX1

OrganismNot specified

UniProt Q08235

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain b； UniProt 1–291 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5Z1G Structure of the Brx1 and Ebp2 complex Deposited 2017-12-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 26–259（234 aa） Fragment：UNP residues 26-259
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M Bis-Tris, pH 5.5 and 1.8M ammonium sulfate
Resolution 2.29 Å R-free 0.297
5Z1G Structure of the Brx1 and Ebp2 complex Deposited 2017-12-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 26–259（234 aa） Fragment：UNP residues 26-259
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M Bis-Tris, pH 5.5 and 1.8M ammonium sulfate
Resolution 2.29 Å R-free 0.297
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain a 1–291（291 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6CB1 Yeast nucleolar pre-60S ribosomal subunit (state 3) Deposited 2018-02-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 37 PDB declaration: 40-meric
Chain b 1–291（291 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain A 1–291（291 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain A 1–291（291 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain A 1–291（291 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain A 1–291（291 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain A 1–291（291 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain A 1–291（291 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain A 1–291（291 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain A 1–291（291 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain A 1–291（291 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain A 1–291（291 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7R6K State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region Deposited 2021-06-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 15 PDB declaration: hexadecameric
Chain A 1–291（291 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain A 1–291（291 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7R7C State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: undecameric
Chain A 1–291（291 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.71 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain A 1–291（291 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain A 1–291（291 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain A 1–291（291 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å

19 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BRX1_YEAST
Isoform —
PDB entities 14
Chains and sequence ranges Author chain b； PDBConstruct 1–291； UniProt 1–291

60S ribosomal protein L32

OrganismNot specified

UniProt P38061

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain e； UniProt 1–130 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 72 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 72 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain 82 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 82 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V4B Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map. Deposited 2004-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain B0 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane
Resolution 11.70 Å
4V6I Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome Deposited 2010-10-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain Bh 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain d 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 73-meric
Chain Bb 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 355 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric
Chain Db 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 360 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Be 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain De 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain Be 2–130（129 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Be 2–130（129 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain e 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain e 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain O2 2–130（129 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain o2 2–130（129 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain O2 2–130（129 aa）
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain O2 2–130（129 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain o2 2–130（129 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain o2 2–130（129 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain O2 2–130（129 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–130（129 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain o2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain g 1–130（130 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain e 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–128（127 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o2 2–128（127 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain e 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain JA 1–130（130 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain JA 1–130（130 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain JA 1–130（130 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain JA 1–130（130 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain JA 1–130（130 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O2 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain o2 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain e5 2–128（127 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain BG 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain AF 2–128（127 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DG 2–128（127 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain o2 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain o2 2–128（127 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain O2 2–128（127 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain o2 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O2 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain O2 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain o2 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain AF 2–128（127 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain DG 2–128（127 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain r 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain r 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AF 2–128（127 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DG 2–128（127 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O2 2–128（127 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain o2 2–128（127 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain O2 2–128（127 aa）
Chain o2 2–128（127 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain i 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain e 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain e 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain e 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain e 2–128（127 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain e 2–128（127 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain e 2–128（127 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain g 1–130（130 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AF 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DG 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain BG 2–128（127 aa）
Chain YG 2–128（127 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain e 1–130（130 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain e 1–130（130 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain e 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain r 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain r 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain r 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain e 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain BG 2–128（127 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain g 2–128（127 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain g 2–128（127 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain g 2–128（127 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ag 2–130（129 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain al 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain BG 1–130（130 aa）
Chain YG 1–130（130 aa）
Chain ZG 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Le 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Le 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Le 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain P 1–130（130 aa）
Chain ey 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain BG 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain BG 2–128（127 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain e 5–126（122 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain e 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Le 1–130（130 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Le 1–130（130 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain r 1–130（130 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain La 2–128（127 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain e 1–130（130 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain e 1–130（130 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ae 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ae 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ae 2–128（127 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Lg 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lg 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain e 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain e 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain e 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHT Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 27-meric
Chain e 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OHY Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain e 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain e 1–130（130 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain e 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain e 1–130（130 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain e 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain e 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain e 1–130（130 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain Bf 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain Ed 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Lh 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain R 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain R 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGU Yeast RQC complex in state E Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain R 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain R 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain R 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain R 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain R 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain Le 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Le 2–128（127 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Q 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Q 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain Q 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain Q 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain Q 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain Q 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Q 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain Q 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Q 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain Q 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain eH 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain Le 1–130（130 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Le 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AF 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DG 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AF 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain DG 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RE 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RE 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RE 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain AF 1–130（130 aa）
Chain DG 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RE 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AF 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain DG 1–130（130 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain Lg 2–128（127 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lg 2–128（127 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain e 1–130（130 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain e 1–130（130 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain e 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain g 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain Le 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain g 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain g 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain g 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain g 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain Lg 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain Lg 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Lg 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Lg 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Lg 2–128（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Ae 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Ae 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain Q 1–130（130 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain Lm 1–130（130 aa）
Chain Mm 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric
Chain R 1–130（130 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain Ae 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9QJC Yeast pre-60S Domain II intermediate Deposited 2025-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain e 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain Le 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain Le 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

198 other PDB entries and 237 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL32_YEAST
Isoform —
PDB entities 15
Chains and sequence ranges Author chain e； PDBConstruct 1–130； UniProt 1–130

60S ribosomal protein L33-A

OrganismNot specified

UniProt P05744

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain f； UniProt 1–107 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 73 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 73 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain 83 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 83 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V6I Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome Deposited 2010-10-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain Bj 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain e 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Bf 1–107（107 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain Df 1–107（107 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain Bf 2–107（106 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Bf 2–107（106 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain f 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain f 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain O3 2–107（106 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain o3 2–107（106 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain O3 2–107（106 aa）
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain O3 2–107（106 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain o3 2–107（106 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain o3 2–107（106 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain O3 2–107（106 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain h 1–107（107 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain f 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o3 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain f 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain KA 1–107（107 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain KA 1–107（107 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain KA 1–107（107 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain KA 1–107（107 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain KA 1–107（107 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain f5 2–107（106 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain BK 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain AG 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DH 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain o3 2–107（106 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain O3 2–107（106 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain o3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain AG 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain DH 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain s 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain s 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AG 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DH 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O3 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain o3 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain O3 2–107（106 aa）
Chain o3 2–107（106 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain j 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6CB1 Yeast nucleolar pre-60S ribosomal subunit (state 3) Deposited 2018-02-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 37 PDB declaration: 40-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain f 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain f 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain f 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain f 2–107（106 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain f 2–107（106 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain f 2–107（106 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain h 1–107（107 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AG 1–107（107 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DH 1–107（107 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain BK 2–107（106 aa）
Chain YK 2–107（106 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain f 1–107（107 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain f 1–107（107 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain f 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain s 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain s 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain s 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain f 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain BK 2–107（106 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain h 2–107（106 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain h 2–107（106 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain h 2–107（106 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ah 2–107（106 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain ak 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain BK 1–107（107 aa）
Chain YK 1–107（107 aa）
Chain ZK 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lf 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Lf 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lf 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain Q 1–107（107 aa）
Chain fy 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain BK 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain BK 2–107（106 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain f 2–106（105 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XIQ Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6XIR Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 76-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain f 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Lf 1–107（107 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Lf 1–107（107 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain v 1–107（107 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lb 2–107（106 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain f 1–107（107 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain f 1–107（107 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Af 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Af 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Af 2–107（106 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Lh 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lh 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain f 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain f 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain f 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHT Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 27-meric
Chain f 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OHY Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL33 1–107（107 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7TOP Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL33 1–107（107 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain f 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain f 1–107（107 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain f 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain f 1–107（107 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain f 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain f 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain f 1–107（107 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZPQ Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) Deposited 2022-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Be 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7ZRS Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map Deposited 2022-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Be 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain Bg 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUW Structure of RQT (C1) bound to the stalled ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Be 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain Ee 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Li 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain S 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain S 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGU Yeast RQC complex in state E Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain S 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain S 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain S 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain S 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain S 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain Lf 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Lf 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8BN3 Yeast 80S, ES7s delta, eIF5A, Stm1 containing Deposited 2022-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain O3 2–107（106 aa）
Not recorded MG MAGNESIUM ION × 220 K POTASSIUM ION × 72 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 SPD SPERMIDINE × 3 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.40 Å
8BQD Yeast 80S ribosome in complex with Map1 (conformation 1) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain BK 2–107（106 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain BK 2–107（106 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain R 1–107（107 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain R 1–107（107 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain R 1–107（107 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain R 1–107（107 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain R 1–107（107 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain R 1–107（107 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain R 1–107（107 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain R 1–107（107 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain R 1–107（107 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain R 1–107（107 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8EUB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I Deposited 2022-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8EVP Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
8EVQ Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 241 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8EVR Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 217 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 W9C (1S,3S,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-alpha-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(propan-2-yl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EVS Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 254 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
8EVT Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) refined against a composite map Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 272 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8EWB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 242 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EWC Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure II Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 247 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain f7 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain Lf 1–107（107 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Lf 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AG 1–107（107 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DH 1–107（107 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AG 1–107（107 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain DH 1–107（107 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RF 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RF 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RF 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain AG 1–107（107 aa）
Chain DH 1–107（107 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RF 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AG 1–107（107 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain DH 1–107（107 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8T2X Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 181 K POTASSIUM ION × 23 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8T2Y Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 197 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8T2Z Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POST Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Af 1–107（107 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8T30 Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain Af 1–107（107 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8T3A Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, sordarin, and hibernating factor Los2 Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Af 1–107（107 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
8T3B Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Af 1–107（107 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8T3C Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Af 1–107（107 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
8T3D Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Af 1–107（107 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8T3E Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure IV Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Af 1–107（107 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8T3F Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Af 1–107（107 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain Lh 2–107（106 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lh 2–107（106 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain f 1–107（107 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain f 1–107（107 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain f 1–107（107 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain h 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain Lf 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain h 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain h 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain h 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain h 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain Lh 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain Lh 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Lh 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Lh 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Lh 2–107（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain R 1–107（107 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain Ll 1–107（107 aa）
Chain Ml 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric
Chain S 1–107（107 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain Af 1–107（107 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9QJC Yeast pre-60S Domain II intermediate Deposited 2025-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain f 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain Lf 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain Lf 1–107（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

225 other PDB entries and 263 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL33A_YEAST
Isoform —
PDB entities 16
Chains and sequence ranges Author chain f； PDBConstruct 1–107； UniProt 1–107

60S ribosomal protein L36-A

OrganismNot specified

UniProt P05745

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain i； UniProt 1–100 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 76 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 76 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain 86 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 86 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V6I Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome Deposited 2010-10-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain Bk 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain g 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Bi 1–100（100 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain Di 1–100（100 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain Bi 2–100（99 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Bi 2–100（99 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain i 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain i 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain O6 2–100（99 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain o6 2–100（99 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain O6 2–100（99 aa）
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain O6 2–100（99 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain o6 2–100（99 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain o6 2–100（99 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain O6 2–100（99 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain k 1–100（100 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain i 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain o6 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain i 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain NA 1–100（100 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain NA 1–100（100 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain NA 1–100（100 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain NA 1–100（100 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain NA 1–100（100 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain i5 2–100（99 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain AC 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain AJ 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DK 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain o6 2–100（99 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain O6 2–100（99 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain o6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain AJ 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain DK 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain v 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain v 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AJ 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DK 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain O6 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain o6 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain O6 2–100（99 aa）
Chain o6 2–100（99 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain m 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6CB1 Yeast nucleolar pre-60S ribosomal subunit (state 3) Deposited 2018-02-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 37 PDB declaration: 40-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain i 2–100（99 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain i 2–100（99 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain i 2–100（99 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain k 1–100（100 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AJ 1–100（100 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DK 1–100（100 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain AC 2–100（99 aa）
Chain XC 2–100（99 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain i 1–100（100 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain i 1–100（100 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain i 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain v 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain v 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain v 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain i 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain AC 1–100（100 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QIK Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-01-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain h 1–100（100 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6QT0 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain h 1–100（100 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6QTZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-02-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain h 1–100（100 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain k 2–100（99 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain k 2–100（99 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain k 2–100（99 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6RI5 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-04-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain h 1–100（100 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6RZZ Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain h 1–100（100 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6S05 Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles Deposited 2019-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain h 1–100（100 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ak 2–100（99 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain ah 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain AC 1–100（100 aa）
Chain XC 1–100（100 aa）
Chain zC 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Li 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Li 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Li 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain T 1–100（100 aa）
Chain ib 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain AC 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AC 2–100（99 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain i 3–100（98 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XIQ Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6XIR Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 76-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain i 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Li 1–100（100 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Li 1–100（100 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain d 1–100（100 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Le 2–100（99 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain i 1–100（100 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain i 1–100（100 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ai 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ai 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Ai 2–100（99 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Lk 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lk 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain i 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain i 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain i 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OSA Pre-translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands Deposited 2021-06-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain eL36 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 490 ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG10K, KSCN, TRIS-HAC
Resolution 3.00 Å R-free 0.250
7OSM Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands Deposited 2021-06-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain eL36 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 499 ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 6000, KSCN, Tris-HAc
Resolution 3.00 Å R-free 0.284
7R6K State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region Deposited 2021-06-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 15 PDB declaration: hexadecameric
Chain i 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
7R6Q State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model Deposited 2021-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain i 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7RR5 Structure of ribosomal complex bound with Rbg1/Tma46 Deposited 2021-08-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain Li 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 286 ASP ASPARTIC ACID × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL36 1–100（100 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7TOP Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL36 1–100（100 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain i 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain i 1–100（100 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain i 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain i 1–100（100 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain i 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain i 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain i 1–100（100 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZPQ Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) Deposited 2022-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Bh 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7ZRS Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map Deposited 2022-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Bh 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain Bj 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUW Structure of RQT (C1) bound to the stalled ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Bh 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain Eh 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Ll 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain V 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain V 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGU Yeast RQC complex in state E Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain V 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain V 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain V 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain V 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain V 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain Li 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain Li 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8BN3 Yeast 80S, ES7s delta, eIF5A, Stm1 containing Deposited 2022-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain O6 2–100（99 aa）
Not recorded MG MAGNESIUM ION × 220 K POTASSIUM ION × 72 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 SPD SPERMIDINE × 3 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.40 Å
8BQD Yeast 80S ribosome in complex with Map1 (conformation 1) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AC 2–100（99 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AC 2–100（99 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain U 1–100（100 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain U 1–100（100 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain U 1–100（100 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain U 1–100（100 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain U 1–100（100 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain U 1–100（100 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain U 1–100（100 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain U 1–100（100 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain U 1–100（100 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain U 1–100（100 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8EUB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I Deposited 2022-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8EVP Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
8EVQ Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 241 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8EVR Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 217 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 W9C (1S,3S,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-alpha-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(propan-2-yl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EVS Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 254 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
8EVT Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) refined against a composite map Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 272 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8EWB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 242 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EWC Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure II Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 247 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain ia 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain Li 1–100（100 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Li 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AJ 1–100（100 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain DK 1–100（100 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AJ 1–100（100 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain DK 1–100（100 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RI 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RI 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RI 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain AJ 1–100（100 aa）
Chain DK 1–100（100 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain RI 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AJ 1–100（100 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain DK 1–100（100 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8T2X Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 181 K POTASSIUM ION × 23 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8T2Y Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 197 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8T2Z Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POST Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Ai 1–100（100 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8T30 Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain Ai 1–100（100 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8T3A Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, sordarin, and hibernating factor Los2 Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain Ai 1–100（100 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
8T3B Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Ai 1–100（100 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8T3C Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Ai 1–100（100 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
8T3D Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Ai 1–100（100 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8T3E Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure IV Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Ai 1–100（100 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8T3F Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Ai 1–100（100 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain Lk 2–100（99 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lk 2–100（99 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain i 1–100（100 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain i 1–100（100 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain i 1–100（100 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain k 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain Li 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain k 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain k 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain k 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain k 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain Lk 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain Lk 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Lk 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain Lk 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Lk 2–100（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain U 1–100（100 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain Li 1–100（100 aa）
Chain Mi 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric
Chain V 1–100（100 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain Ai 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain Li 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain Li 1–100（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

223 other PDB entries and 261 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL36A_YEAST
Isoform —
PDB entities 17
Chains and sequence ranges Author chain i； PDBConstruct 1–100； UniProt 1–100

rRNA-processing protein EBP2

OrganismNot specified

UniProt P36049

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain m； UniProt 1–427 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5Z1G Structure of the Brx1 and Ebp2 complex Deposited 2017-12-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 186–295（110 aa） Fragment：UNP residues 186-295
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M Bis-Tris, pH 5.5 and 1.8M ammonium sulfate
Resolution 2.29 Å R-free 0.297
5Z1G Structure of the Brx1 and Ebp2 complex Deposited 2017-12-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 186–295（110 aa） Fragment：UNP residues 186-295
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M Bis-Tris, pH 5.5 and 1.8M ammonium sulfate
Resolution 2.29 Å R-free 0.297
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 1–427（427 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain J 1–427（427 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain J 1–427（427 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain J 1–427（427 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain J 1–427（427 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain J 1–427（427 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain J 1–427（427 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain J 1–427（427 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain J 1–427（427 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain J 1–427（427 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7R6K State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region Deposited 2021-06-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 15 PDB declaration: hexadecameric
Chain J 1–427（427 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain J 1–427（427 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain J 1–427（427 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain J 1–427（427 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain J 1–427（427 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å

16 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EBP2_YEAST
Isoform —
PDB entities 18
Chains and sequence ranges Author chain m； PDBConstruct 1–427； UniProt 1–427

Pescadillo homolog

OrganismNot specified

UniProt P53261

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain n； UniProt 1–605 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain M 1–605（605 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain n 1–605（605 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain n 1–605（605 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain n 1–605（605 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain n 1–605（605 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain n 1–605（605 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7R6Q State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model Deposited 2021-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain n 1–605（605 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain n 1–605（605 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain n 1–605（605 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain n 1–605（605 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain n 1–605（605 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain n 1–605（605 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain n 1–605（605 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain n 1–605（605 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain n 1–605（605 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å

27 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PESC_YEAST
Isoform —
PDB entities 19
Chains and sequence ranges Author chain n； PDBConstruct 1–605； UniProt 1–605

Ribosome biogenesis protein 15

OrganismNot specified

UniProt P53927

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain o； UniProt 1–220 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
5T9P Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate Deposited 2016-09-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 81–191（111 aa） Fragment：residues 81-191
Not recorded SO4 SULFATE ION × 5 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；295 K；18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600
Resolution 2.00 Å R-free 0.236
5T9P Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate Deposited 2016-09-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 81–191（111 aa） Fragment：residues 81-191
Not recorded SO4 SULFATE ION × 4 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；295 K；18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600
Resolution 2.00 Å R-free 0.236
5T9P Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate Deposited 2016-09-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 81–191（111 aa） Fragment：residues 81-191
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；295 K；18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600
Resolution 2.00 Å R-free 0.236
5T9P Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate Deposited 2016-09-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 81–191（111 aa） Fragment：residues 81-191
Not recorded SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；295 K；18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600
Resolution 2.00 Å R-free 0.236
5T9P Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate Deposited 2016-09-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 81–191（111 aa） Fragment：residues 81-191
Chain B 81–191（111 aa） Fragment：residues 81-191
Not recorded SO4 SULFATE ION × 6 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；295 K；18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600
Resolution 2.00 Å R-free 0.236
5T9P Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate Deposited 2016-09-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 81–191（111 aa） Fragment：residues 81-191
Chain D 81–191（111 aa） Fragment：residues 81-191
Not recorded SO4 SULFATE ION × 5 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；295 K；18% (w/v) PEG 4000, 0.2 M ammonium sulfate, pH 5.25 and 9% (v/v) Jeffamine 600
Resolution 2.00 Å R-free 0.236
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain E 1–220（220 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6CB1 Yeast nucleolar pre-60S ribosomal subunit (state 3) Deposited 2018-02-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 37 PDB declaration: 40-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain o 1–220（220 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain o 1–220（220 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain o 1–220（220 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain o 1–220（220 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain o 1–220（220 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain o 1–220（220 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7R6Q State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model Deposited 2021-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain o 1–220（220 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain o 1–220（220 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain o 1–220（220 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain o 1–220（220 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain o 1–220（220 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain o 1–220（220 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain o 1–220（220 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain o 1–220（220 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain o 1–220（220 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å

32 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOP15_YEAST
Isoform —
PDB entities 20
Chains and sequence ranges Author chain o； PDBConstruct 1–220； UniProt 1–220

ATP-dependent RNA helicase HAS1

OrganismNot specified

UniProt Q03532

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain p； UniProt 1–505 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain Y 1–505（505 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain p 1–505（505 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain D 1–505（505 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain D 1–505（505 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain D 1–505（505 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain D 1–505（505 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain D 1–505（505 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain D 1–505（505 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain D 1–505（505 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain D 1–505（505 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain D 1–505（505 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain D 1–505（505 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain D 1–505（505 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain D 1–505（505 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7R6Q State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model Deposited 2021-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain D 1–505（505 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain D 1–505（505 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain D 1–505（505 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain D 1–505（505 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain D 1–505（505 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HAS1_YEAST
Isoform —
PDB entities 21
Chains and sequence ranges Author chain p； PDBConstruct 1–505； UniProt 1–505

Ribosome biogenesis protein ERB1

OrganismNot specified

UniProt Q04660

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain s； UniProt 1–807 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4U7A The carboxy-terminal domain of Erb1 is a seven-bladed beta-propeller that binds RNA. Deposited 2014-07-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain A 1–807（807 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 EOH ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；10% PEG 8000, 8% ethylene glycol, 0.1M Hepes pH 7.5, 3% ethanol
Resolution 1.60 Å R-free 0.174
6CB1 Yeast nucleolar pre-60S ribosomal subunit (state 3) Deposited 2018-02-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 37 PDB declaration: 40-meric
Chain s 372–807（436 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain m 1–807（807 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain m 1–807（807 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain B 1–807（807 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain H 1–807（807 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain m 1–807（807 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain m 1–807（807 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain m 1–807（807 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain m 1–807（807 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain m 1–807（807 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain m 1–807（807 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain m 1–807（807 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain m 1–807（807 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7R6K State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region Deposited 2021-06-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 15 PDB declaration: hexadecameric
Chain m 1–807（807 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
7R6Q State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model Deposited 2021-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain m 1–807（807 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain m 1–807（807 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain m 1–807（807 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain m 1–807（807 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain m 1–807（807 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ERB1_YEAST
Isoform —
PDB entities 22
Chains and sequence ranges Author chain s； PDBConstruct 1–807； UniProt 1–807

Ribosome biogenesis protein RLP7

OrganismNot specified

UniProt P40693

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain t； UniProt 1–322 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosomal RNA-processing protein 1 × 1 （P35178） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain r 1–322（322 aa）
Chain s 1–322（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain D 1–322（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6CB1 Yeast nucleolar pre-60S ribosomal subunit (state 3) Deposited 2018-02-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 37 PDB declaration: 40-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain t 1–322（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain t 1–322（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain t 1–322（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain t 1–322（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain t 1–322（322 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain t 1–322（322 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7R6Q State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model Deposited 2021-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain t 1–322（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
7R72 State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 local model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain t 1–322（322 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain t 1–322（322 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain t 1–322（322 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain t 2–322（321 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain t 1–322（322 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain t 1–322（322 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain t 1–322（322 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å

32 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RLP7_YEAST
Isoform —
PDB entities 23
Chains and sequence ranges Author chain t； PDBConstruct 1–322； UniProt 1–322

Ribosomal RNA-processing protein 1

OrganismNot specified

UniProt P35178

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain z； UniProt 1–278 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） 60S ribosomal protein L16-A × 1 （P26784） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain X 1–278（278 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain z 1–278（278 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6CB1 Yeast nucleolar pre-60S ribosomal subunit (state 3) Deposited 2018-02-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 37 PDB declaration: 40-meric
Chain z 1–278（278 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain 4 1–278（278 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain 4 1–278（278 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain 4 1–278（278 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain 4 1–278（278 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain 4 1–278（278 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain 4 1–278（278 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain 4 1–278（278 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain w 1–278（278 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain w 1–278（278 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9QJC Yeast pre-60S Domain II intermediate Deposited 2025-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain z 1–278（278 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RRP1_YEAST
Isoform —
PDB entities 24
Chains and sequence ranges Author chain z； PDBConstruct 1–278； UniProt 1–278

60S ribosomal protein L16-A

OrganismNot specified

UniProt P26784

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 25 RNA 3 PDB declaration: 28-meric（28） Consistent with all polymer counts Chain O； UniProt 1–199 Not recorded Ribosome biogenesis protein MAK21 × 1 （Q12176） NOC2 isoform 1 × 1 （A0A8H4BX61） 60S ribosomal protein L4-A × 1 （P10664） Protein MAK16 × 1 （P10962） 60S ribosomal protein L6-A × 1 （Q02326） 60S ribosomal protein L7-A × 1 （P05737） 60S ribosomal protein L8-A × 1 （P17076） Proteasome-interacting protein CIC1 × 1 （P38779） 60S ribosomal protein L13-A × 1 （Q12690） 60S ribosomal protein L14-A × 1 （P36105） 60S ribosomal protein L15-A × 1 （P05748） 60S ribosomal protein L18-A × 1 （P0CX49） 60S ribosomal protein L20-A × 1 （P0CX23） Ribosome biogenesis protein BRX1 × 1 （Q08235） 60S ribosomal protein L32 × 1 （P38061） 60S ribosomal protein L33-A × 1 （P05744） 60S ribosomal protein L36-A × 1 （P05745） rRNA-processing protein EBP2 × 1 （P36049） Pescadillo homolog × 1 （P53261） Ribosome biogenesis protein 15 × 1 （P53927） ATP-dependent RNA helicase HAS1 × 1 （Q03532） Ribosome biogenesis protein ERB1 × 1 （Q04660） Ribosome biogenesis protein RLP7 × 1 （P40693） Ribosomal RNA-processing protein 1 × 1 （P35178） 25S ribosomal RNA × 1 5.8S ribosomal RNA × 1 ITS2 ribosomal RNA × 1 MG MAGNESIUM ION × 33 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8E5T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 56 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain 56 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
Resolution 6.10 Å
3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain 66 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.20 Å
3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 66 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
Resolution 6.30 Å
3JCT Cryo-em structure of eukaryotic pre-60S ribosomal subunits Deposited 2016-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.245
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.237
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.90 Å R-free 0.245
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.60 Å R-free 0.267
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.255
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 2.80 Å R-free 0.246
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.259
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.245
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.262
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.253
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.00 Å R-free 0.258
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.255
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.20 Å R-free 0.246
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.45 Å R-free 0.260
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.247
4V4B Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map. Deposited 2004-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain BM 1–146（146 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane
Resolution 11.70 Å
4V6I Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome Deposited 2010-10-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain BK 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
4V7F Arx1 pre-60S particle. Deposited 2013-12-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain J 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 73-meric
Chain BP 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 355 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V7R Yeast 80S ribosome. Deposited 2010-07-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric
Chain DP 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 360 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
Resolution 4.00 Å R-free 0.341
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain BO 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain DO 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 688 MG MAGNESIUM ION × 1170 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.229
4V8T Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 Deposited 2012-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2；pH 8；20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE
Resolution 8.10 Å
4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain BO 2–199（198 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 191 OHX osmium (III) hexammine × 197 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 4.30 Å
4V8Z Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric
Chain BO 2–199（198 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 226 OHX osmium (III) hexammine × 210 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT；pH 7.2；3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING,
Resolution 6.60 Å
5APN Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain O 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM；pH 8；20MM
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.91 Å
5APO Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1 Deposited 2015-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain O 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 280 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL；pH 8；20MM HEPES-KOH, 100mM NACL, 5mM MGCL2, 5mM BETA-MERCAPTOETHANOL
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；PLUNGE-FROZEN
Resolution 3.41 Å
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.15 Å R-free 0.252
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain M6 2–199（198 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric
Chain m6 2–199（198 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.25 Å R-free 0.301
5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric
Chain M6 2–199（198 aa）
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.45 Å R-free 0.263
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC
Chain M6 2–199（198 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC
Chain m6 2–199（198 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.30 Å R-free 0.310
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC
Chain m6 2–199（198 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC
Chain M6 2–199（198 aa）
Not recorded ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.10 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 2–199（198 aa）
Not recorded OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.40 Å R-free 0.284
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric
Chain m6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 2–199（198 aa）
Not recorded MG MAGNESIUM ION × 462 OHX osmium (III) hexammine × 500 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
Resolution 3.10 Å R-free 0.291
5GAK Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric
Chain Q 1–199（199 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Details can be retrieved from EMD-3227
Resolution 3.88 Å
5H4P Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1 Deposited 2016-11-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain O 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 3–199（197 aa）
Not recorded OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric
Chain m6 3–199（197 aa）
Not recorded OHX osmium (III) hexammine × 512 MG MAGNESIUM ION × 526 ZN ZINC ION × 8 UAM Amicoumacin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.251
5JCS CRYO-EM STRUCTURE OF THE RIX1-REA1 PRE-60S PARTICLE Deposited 2016-04-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain O 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
5JUO Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I (fully rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain T 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain T 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain T 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 4.20 Å
5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain T 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain T 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M6 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m6 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 1166 OHX osmium (III) hexammine × 686 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
Resolution 3.25 Å R-free 0.249
5M1J Nonstop ribosomal complex bound with Dom34 and Hbs1 Deposited 2016-10-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain K5 3–199（197 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain AU 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain w 3–199（197 aa）
Not recorded OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CQ 3–199（197 aa）
Not recorded OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.50 Å R-free 0.239
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain m6 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.253
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain m6 3–199（197 aa）
Not recorded PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain M6 3–199（197 aa）
Not recorded PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.30 Å R-free 0.250
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain m6 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain M6 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.70 Å R-free 0.235
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC
Chain M6 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC
Chain m6 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.40 Å R-free 0.238
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric
Chain w 3–199（197 aa）
Not recorded OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric
Chain CQ 3–199（197 aa）
Not recorded OHX osmium (III) hexammine × 549 MG MAGNESIUM ION × 758 HN8 Haemanthamine × 1 GOL GLYCEROL × 3 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.252
5T62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain b 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 160 K POTASSIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain b 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain w 3–199（197 aa）
Not recorded OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CQ 3–199（197 aa）
Not recorded OHX osmium (III) hexammine × 556 MG MAGNESIUM ION × 728 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
Resolution 3.00 Å R-free 0.227
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain M6 3–199（197 aa）
Not recorded OHX osmium (III) hexammine × 659 MG MAGNESIUM ION × 1026 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGA Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain m6 3–199（197 aa）
Not recorded OHX osmium (III) hexammine × 686 MG MAGNESIUM ION × 1166 ZN ZINC ION × 8 PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG20000
Resolution 3.30 Å R-free 0.265
5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric
Chain M6 3–199（197 aa）
Chain m6 3–199（197 aa）
Not recorded OHX osmium (III) hexammine × 1095 MG MAGNESIUM ION × 1191 ZN ZINC ION × 16 PHE PHENYLALANINE × 2 LEU LEUCINE × 2 SPS SPARSOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG20000
Resolution 3.50 Å R-free 0.312
5Z3G Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP) Deposited 2018-01-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric
Chain S 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1-3 seconds before plunging
Resolution 3.65 Å
6C0F Yeast nucleolar pre-60S ribosomal subunit (state 2) Deposited 2017-12-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ELZ State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6EM1 State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6EM3 State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 33-meric
Chain O 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6EM4 State B architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain O 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6EM5 State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes Deposited 2017-10-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain O 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6FT6 Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors Deposited 2018-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain O 3–199（197 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.40 Å
6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain O 3–199（197 aa）
Not recorded ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 3.90 Å
6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain O 3–199（197 aa）
Not recorded ZN ZINC ION × 8 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 4, blot waiting time 30 s
Resolution 4.00 Å
6HD7 Cryo-EM structure of the ribosome-NatA complex Deposited 2018-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric
Chain Q 1–199（199 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain w 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CQ 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Resolution 3.10 Å R-free 0.264
6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric
Chain AU 3–199（197 aa）
Chain XU 3–199（197 aa）
Not recorded ZN ZINC ION × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6M62 Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state. Deposited 2020-03-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N8J Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain O 1–199（199 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8K Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain O 1–199（199 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8L Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain O 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain b 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N8N Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain b 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6N8O Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit Deposited 2018-11-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain b 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OIG Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2019-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain O 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Q8Y Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex Deposited 2018-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain AU 3–199（197 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6R84 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric
Chain Q 3–199（197 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6R86 Yeast Vms1-60S ribosomal subunit complex (post-state) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric
Chain Q 3–199（197 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6R87 Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1) Deposited 2019-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric
Chain Q 3–199（197 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AQ 2–199（198 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.28 Å
6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain u 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6SV4 The cryo-EM structure of SDD1-stalled collided trisome. Deposited 2019-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric
Chain AU 1–199（199 aa）
Chain XU 1–199（199 aa）
Chain zU 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6T4Q Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Deposited 2019-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LO 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6T7I Structure of yeast 80S ribosome stalled on the CGA-CGA inhibitory codon combination. Deposited 2019-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LO 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6T7T Structure of yeast 80S ribosome stalled on poly(A) tract. Deposited 2019-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LO 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T83 Structure of yeast disome (di-ribosome) stalled on poly(A) tract. Deposited 2019-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric
Chain Oy 1–199（199 aa）
Chain Qa 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6TB3 yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex Deposited 2019-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain AU 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 327 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6TNU Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Deposited 2019-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AU 3–199（197 aa）
Not recorded ZN ZINC ION × 7 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6WOO CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP Deposited 2020-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain O 3–199（197 aa）
Not recorded ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 U6A N-carboxy-L-threonine × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XIQ Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6XIR Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Deposited 2020-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 76-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6YLG Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6YLH Rix1-Rea1 pre-60S particle - full composite structure Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6YLX pre-60S State NE1 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain O 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6YLY pre-60S State NE2 (TAP-Flag-Nop53) Deposited 2020-04-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LO 1–199（199 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6Z6K Cryo-EM structure of yeast reconstituted Lso2 bound to 80S ribosomes Deposited 2020-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain LO 1–199（199 aa）
Not recorded ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7AZY Context-specific inhibition of eukaryotic translation by macrolide antibiotics Deposited 2020-11-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain V 1–199（199 aa）
Not recorded TEL TELITHROMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LQ 3–199（197 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
7BT6 Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain O 1–199（199 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7BTB Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2) Deposited 2020-04-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain O 1–199（199 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AO 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 366 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AO 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 745 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain AO 3–199（197 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 374 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7NAC State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model Deposited 2021-06-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7NRC Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LQ 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LQ 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.36 Å
7OF1 Nog1-TAP associated immature ribosomal particle population A from S. cerevisiae Deposited 2021-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric
Chain O 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OH3 Nog1-TAP associated immature ribosomal particle population B from S. cerevisiae Deposited 2021-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain O 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHP Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHQ Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric
Chain O 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OHR Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.72 Å
7OHS Nog1-TAP associated immature ribosomal particle population F from S. cerevisiae Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
7OHT Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 27-meric
Chain O 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
7OHU Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OHV Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7OHW Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 40-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OHX Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population A Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OHY Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL34 expression shut down, population B Deposited 2021-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7R7A State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model Deposited 2021-06-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL16 1–199（199 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7TOP Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 Deposited 2022-01-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric
Chain AL16 1–199（199 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7U0H State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model Deposited 2022-02-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain O 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7UG6 Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain O 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；One blotting step of 2 seconds at force 0
Resolution 2.90 Å
7UOO Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state Deposited 2022-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain O 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.34 Å
7UQB Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1-D52A strain with AlF4 Deposited 2022-04-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain O 1–199（199 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 MG MAGNESIUM ION × 81 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
7UQZ Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain Deposited 2022-04-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain O 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7V08 Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain Deposited 2022-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain O 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 81 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 2 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
7Z34 Structure of pre-60S particle bound to DRG1(AFG2). Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain O 1–199（199 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 11 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7ZPQ Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) Deposited 2022-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BN 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7ZRS Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map Deposited 2022-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BN 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7ZS5 Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain BP 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7ZUW Structure of RQT (C1) bound to the stalled ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain BN 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain EN 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 86 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain LR 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 324 SPD SPERMIDINE × 1 ZN ZINC ION × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AAF Yeast RQC complex in state G Deposited 2022-07-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain B 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8AGT Yeast RQC complex in state F Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain B 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGU Yeast RQC complex in state E Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric
Chain B 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8AGV Yeast RQC complex in state H Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain B 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGW Yeast RQC complex in state D Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric
Chain B 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8AGX Yeast RQC complex in state with the RING domain of Ltn1 in the IN position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric
Chain B 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8AGZ Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric
Chain B 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 13 ZN ZINC ION × 7 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8BIP Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain LO 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BJQ Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain LO 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 206 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8BN3 Yeast 80S, ES7s delta, eIF5A, Stm1 containing Deposited 2022-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain M6 3–199（197 aa）
Not recorded MG MAGNESIUM ION × 220 K POTASSIUM ION × 72 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 SPD SPERMIDINE × 3 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.40 Å
8BQD Yeast 80S ribosome in complex with Map1 (conformation 1) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AU 3–199（197 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain AU 3–199（197 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain A 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.97 Å
8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain A 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain A 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.04 Å
8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain A 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.05 Å
8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain A 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain A 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain A 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain A 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain A 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain A 1–199（199 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 153 K POTASSIUM ION × 10 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
8EUB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure I Deposited 2022-10-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8EVP Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
8EVQ Hypopseudouridylated Ribosome bound with TSV IRES, eEF2, GDP, and sordarin, Structure I Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 241 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8EVR Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 217 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 W9C (1S,3S,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-alpha-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(propan-2-yl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EVS Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 254 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
8EVT Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) refined against a composite map Deposited 2022-10-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 272 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8EWB Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 242 ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8EWC Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), Structure II Deposited 2022-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 247 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.45 Å
8HFR NPC-trapped pre-60S particle Deposited 2022-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 61-meric
Chain O6 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 237 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain LO 1–199（199 aa）
Not recorded ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain LO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain w 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain CQ 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 3.16 Å R-free 0.251
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain w 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain CQ 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 519 MG MAGNESIUM ION × 785 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 9 5XU (2~{S})-2-azanylpropanal × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.223
8P8M Yeast 60S ribosomal subunit, RPL39 deletion Deposited 2023-06-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JW 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 156 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.66 Å
8P8N Mouse RPL39 integrated into the yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JW 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 152 CL CHLORIDE ION × 20 SPD SPERMIDINE × 1 SPM SPERMINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.15 Å
8P8U Yeast 60S ribosomal subunit Deposited 2023-06-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JW 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 129 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.23 Å
8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric
Chain CQ 1–199（199 aa）
Chain w 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 930 MG MAGNESIUM ION × 1464 SPD SPERMIDINE × 2 XBI (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-5,5,7,8~{a}-tetramethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 2 ZN ZINC ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å
8PFR Mouse RPL39L integrated into the yeast 60S ribosomal subunit Deposited 2023-06-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric
Chain JW 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 170 CL CHLORIDE ION × 24 SPM SPERMINE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；30s pre-blot incubation
Resolution 2.15 Å
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain w 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain CQ 1–199（199 aa）
Not recorded OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
Resolution 2.90 Å R-free 0.230
8T2X Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger RNA and eIF5A, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 181 K POTASSIUM ION × 23 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8T2Y Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, PRE Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 197 SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8T2Z Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA, messenger RNA, POST Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain AO 1–199（199 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8T30 Hypomethylated yeast 80S bound with cycloheximide, unmodified U2921, mid rotated Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AO 1–199（199 aa）
Not recorded SPD SPERMIDINE × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8T3A Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, sordarin, and hibernating factor Los2 Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric
Chain AO 1–199（199 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
8T3B Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure I Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AO 1–199（199 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8T3C Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure II Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AO 1–199（199 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
8T3D Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AO 1–199（199 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8T3E Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure IV Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AO 1–199（199 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8T3F Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AO 1–199（199 aa）
Not recorded ZN ZINC ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain LQ 3–199（197 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LQ 3–199（197 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
8V83 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain O 1–199（199 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
8V84 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain O 1–199（199 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8V87 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) Deposited 2023-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain O 1–199（199 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
8XU8 State 2c(S2c) of yeast 80S ribosome bound to compact eEF2 and 2 tRNAs during peptidyl transferation Deposited 2024-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain Q 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5；YPD
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0U dormant ribosome with STM1 Deposited 2024-01-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric
Chain LO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 281 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Q 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Q 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain Q 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Q 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 4.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric
Chain LQ 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain LQ 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LQ 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric
Chain LQ 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain LQ 3–199（197 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9DOV Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B Deposited 2024-09-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 257 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9DP7 Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II Deposited 2024-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 247 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9F58 Gcn2 dimer bound to the 60S ribosomal subunit Deposited 2024-04-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain p 1–199（199 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric
Chain LJ 1–199（199 aa）
Chain MJ 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 295 ZN ZINC ION × 13 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric
Chain a0 1–199（199 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric
Chain AO 1–199（199 aa）
Not recorded MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.75 Å
9QJC Yeast pre-60S Domain II intermediate Deposited 2025-03-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain O 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LO 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain LO 1–199（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

220 other PDB entries and 259 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL16A_YEAST
Isoform —
PDB entities 25
Chains and sequence ranges Author chain O； PDBConstruct 1–199； UniProt 1–199

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8e5t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8e5t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8e5t
Deposition date deposition_date2022-08-22
Structure title titleYeast co-transcriptional Noc1-Noc2 RNP assembly checkpoint intermediate
Keywords keywordsCo-transcriptional pre-60S, ribosome biogenesis, early check-point intermediate, RIBOSOME; RIBOSOME
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier86.44 Å
Radius of gyration Rg (electron density) rg_electron88.02 Å
Forward intensity I(0) i015548300000.00
Molecular weight molecular_weight799770.0 kDa
Excluded volume excluded_volume891570 ų
Envelope volume envelope_volume1755400 ų
Hydration-shell volume shell_volume168720 ų
Envelope diameter envelope_diameter319.5 Å
Shell Rg shell_rg79.97 Å
Envelope Rg envelope_rg87.80 Å
Shape Rg shape_rg88.27 Å
Total Rg total_rg87.34 Å
Total atoms total_atoms55125
Residues n_residues6126
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax237.7 Å
Rg (real space) rg_real82.07 Å
Rg uncertainty (real space) rg_real_error0.94 Å
I(0) (real space) i0_real1.4870e+10
I(0) uncertainty (real space) i0_real_error2.9250e+08
Rg (reciprocal space) rg_reciprocal82.97 Å
I(0) (reciprocal space) i0_reciprocal15390000000.0000
Solution quality estimate total_estimate0.9131
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary79.2 Å
Skewness Skewness skewness0.382
Kurtosis Kurtosis kurtosis-0.639
Angular range angular_range— – 0.0900 Å−1
Current regularization parameter α current_alpha1.0670
Highest regularization parameter α highest_alpha535800000.0000
Real-space data points n_real_points19
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.987; Stabil: 0.976; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.002
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (30)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id8e5tD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily110 —
Domain ID domain_id8e5tN01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1120 — Ribosomal protein L15e
Homologous superfamily homologous superfamily10 — Ribosomal protein L15
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8. Citations (1)

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9. Files and Curves (10)