8hte

Crystal structure of an effector mutant in complex with ubiquitin

Method: X-RAY DIFFRACTION D_max: 69.4 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD(+)--protein-threonine ADP-ribosyltransferase

Chromobacterium violaceum ATCC 12472

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 45–276	Mutation：E220A	Ubiquitin × 1 （P0CH08） SO4 SULFATE ION × 2 GOL GLYCEROL × 2 NCA NICOTINAMIDE × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；100 mM BIS-TRIS propane, pH 7.0, and 1.5 M ammonium sulfate	Resolution 2.31 Å R-free 0.228

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 8HTE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8HTC Crystal structure of a SeMet-labeled effector from Chromobacterium violaceum in complex with Ubiquitin Deposited 2022-12-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 45–276（232 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；289 K；100 mM sodium cacodylate, pH 6.25, 200 mM sodium acetate, 22% PEG 8000	Resolution 2.20 Å R-free 0.247
8HTD Crystal structure of an effector from Chromobacterium violaceum in complex with ubiquitin Deposited 2022-12-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 45–276（232 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；100 mM sodium cacodylate, pH 6.5, 200 mM sodium acetate, 28% to 30% PEG 8000	Resolution 1.85 Å R-free 0.225
8HTF Crystal structure of an effector in complex with ubiquitin Deposited 2022-12-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 45–276（232 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；289 K；100 mM sodium cacodylate, pH 6.25, 200 mM sodium acetate, 22% PEG 8000, 25% glycerol	Resolution 2.15 Å R-free 0.223
8UX2 Chromobacterium violaceum mono-ADP-ribosyltransferase CteC in complex with NAD+ Deposited 2023-11-08	Different construct Different mutation/modification 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 36–276（241 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.25M calcium acetate, 20% PEG 3000	Resolution 1.87 Å R-free 0.227
8UX2 Chromobacterium violaceum mono-ADP-ribosyltransferase CteC in complex with NAD+ Deposited 2023-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 36–276（241 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.25M calcium acetate, 20% PEG 3000	Resolution 1.87 Å R-free 0.227
8UX2 Chromobacterium violaceum mono-ADP-ribosyltransferase CteC in complex with NAD+ Deposited 2023-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 36–276（241 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.25M calcium acetate, 20% PEG 3000	Resolution 1.87 Å R-free 0.227

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CTEC_CHRVO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–233； UniProt 45–276

Ubiquitin

Saccharomyces cerevisiae S288C

UniProt P0CH08

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–76	Not recorded	NAD(+)--protein-threonine ADP-ribosyltransferase × 1 （Q7NY09） SO4 SULFATE ION × 2 GOL GLYCEROL × 2 NCA NICOTINAMIDE × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；100 mM BIS-TRIS propane, pH 7.0, and 1.5 M ammonium sulfate	Resolution 2.31 Å R-free 0.228

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8HTE	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 construct Different 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 80 1–128（128 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 construct Different 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 80 1–128（128 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 construct 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 90 1–128（128 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 construct 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: 84-meric	Chain 90 1–128（128 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
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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric	Chain Bp 77–128（52 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
4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11	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 Bm 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain Dm 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric	Chain m 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric	Chain Bm 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric	Chain Bm 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric	Chain m 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric	Chain m 1–128（128 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric	Chain Q0 77–128（52 aa） Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 49-meric	Chain o 1–128（128 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
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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain q0 77–128（52 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
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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric	Chain RA 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric	Chain RA 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric	Chain RA 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric	Chain RA 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric	Chain RA 1–128（128 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric	Chain q0 77–128（52 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 experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric	Chain m5 77–128（52 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric	Chain AO 1–128（128 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric	Chain AN 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric	Chain DO 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric	Chain AN 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric	Chain DO 77–128（52 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric	Chain z 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric	Chain z 1–128（128 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain AN 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric	Chain DO 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric	Chain Q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric	Chain q0 77–128（52 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric	Chain Q0 77–128（52 aa） Chain q0 77–128（52 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
6EF3 Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state) Deposited 2018-08-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain u 1–128（128 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；specimens were manually blotted with Whatman #1 filter paper	Resolution 4.17 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric	Chain m 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric	Chain m 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric	Chain m 77–128（52 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 51-meric	Chain o 1–128（128 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 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 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric	Chain DO 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric	Chain AO 77–128（52 aa） Chain XO 77–128（52 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
6N8M Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit Deposited 2018-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric	Chain z 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric	Chain z 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric	Chain z 1–128（128 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
6OA9 Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Deposited 2019-03-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain H 1–76（76 aa） Chain J 1–76（76 aa） Chain K 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Waited 20 seconds before blotting for 2.5-3 seconds.	Resolution 3.90 Å
6OAA Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1 Deposited 2019-03-15	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 1–76（76 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Waited 20 seconds before blotting for 2.5-3 seconds.	Resolution 4.10 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric	Chain m 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric	Chain AO 77–128（52 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric	Chain t 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric	Chain t 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric	Chain t 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric	Chain o 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 47-meric	Chain o 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 49-meric	Chain o 77–128（52 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric	Chain t 1–128（128 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
6S47 Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 Deposited 2019-06-26	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: 79-meric	Chain Ao 2–128（127 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 construct Different 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 ad 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 225 PDB declaration: 242-meric	Chain AO 1–128（128 aa） Chain XO 1–128（128 aa） Chain zO 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric	Chain Lm 77–128（52 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 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: 81-meric	Chain Lm 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric	Chain Lm 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 149 PDB declaration: 159-meric	Chain X 1–128（128 aa） Chain mb 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric	Chain AO 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric	Chain AO 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric	Chain m 78–128（51 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric	Chain m 1–128（128 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
6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28	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 Lm 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Lm 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric	Chain P 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric	Chain Li 77–128（52 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
7MPI Stm1 bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Am 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Am 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain Am 77–128（52 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
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric	Chain Lo 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric	Chain Lo 77–128（52 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
7TOO Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 Deposited 2022-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric	Chain AL40 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric	Chain AL40 1–128（128 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
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric	Chain Bl 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric	Chain Bl 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric	Chain Bn 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 82-meric	Chain Bl 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric	Chain El 77–128（52 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 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: 86-meric	Chain Lp 77–128（52 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric	Chain Z 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric	Chain Z 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric	Chain Z 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric	Chain Z 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 53-meric	Chain Z 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric	Chain Z 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric	Chain Z 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric	Chain Lm 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric	Chain Lm 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric	Chain Q0 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric	Chain AO 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric	Chain AO 77–128（52 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
8CAH Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex Deposited 2023-01-24	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 48-meric	Chain k 1–76（76 aa）	Not recorded	MG MAGNESIUM ION × 80 ZN ZINC ION × 2 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8CAS Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial) Deposited 2023-01-24	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain y 1–76（76 aa）	Not recorded	ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 2 MET METHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric	Chain Y 1–128（128 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 construct 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 Y 1–128（128 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 construct 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: 84-meric	Chain Y 1–128（128 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 construct 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: 84-meric	Chain Y 1–128（128 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 construct 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: 84-meric	Chain Y 1–128（128 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 construct 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: 84-meric	Chain Y 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric	Chain Y 1–128（128 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 construct 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: 84-meric	Chain Y 1–128（128 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 construct 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 Y 1–128（128 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 construct 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: 80-meric	Chain Y 1–128（128 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
8DAS Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intA) Deposited 2022-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain J 1–76（76 aa） Chain K 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. cryo-EM vitrification conditions Cryogen ETHANE；8 s wait, 4 s blot before plunging	Resolution 3.50 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 construct 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: 82-meric	Chain Am 1–128（128 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 construct Different 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 Am 1–128（128 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 construct 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: 82-meric	Chain Am 1–128（128 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 construct 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: 82-meric	Chain Am 1–128（128 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 construct 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: 82-meric	Chain Am 1–128（128 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 construct Different 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 Am 1–128（128 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 construct 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: 82-meric	Chain Am 1–128（128 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 construct Different 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 Am 1–128（128 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
8HTD Crystal structure of an effector from Chromobacterium violaceum in complex with ubiquitin Deposited 2022-12-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；100 mM sodium cacodylate, pH 6.5, 200 mM sodium acetate, 28% to 30% PEG 8000	Resolution 1.85 Å R-free 0.225
8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric	Chain Lm 1–128（128 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 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: 85-meric	Chain Lm 1–128（128 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 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 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric	Chain DO 1–128（128 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 construct 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 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric	Chain DO 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric	Chain RO 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric	Chain RO 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric	Chain RO 1–128（128 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric	Chain AN 1–128（128 aa） Chain DO 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 40 PDB declaration: 43-meric	Chain RO 1–128（128 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 construct 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 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric	Chain DO 1–128（128 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 construct 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 Am 1–128（128 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 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: 81-meric	Chain Am 1–128（128 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 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: 81-meric	Chain Am 1–128（128 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 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 Am 1–128（128 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 construct 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: 82-meric	Chain Am 1–128（128 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 construct 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: 81-meric	Chain Am 1–128（128 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 construct 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: 81-meric	Chain Am 1–128（128 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 construct 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: 81-meric	Chain Am 1–128（128 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 construct 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: 81-meric	Chain Am 1–128（128 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 construct 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: 81-meric	Chain Am 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric	Chain Lo 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric	Chain Lo 77–128（52 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
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric	Chain o 77–128（52 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 77-meric	Chain Lm 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric	Chain o 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric	Chain o 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric	Chain o 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric	Chain o 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric	Chain Lo 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric	Chain Lo 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric	Chain Lo 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric	Chain Lo 77–128（52 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric	Chain Lo 77–128（52 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 construct Different 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 Am 1–128（128 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 construct Different 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 Am 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain Y 1–128（128 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric	Chain Le 1–128（128 aa） Chain Me 1–128（128 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric	Chain Z 1–128（128 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 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 Am 1–128（128 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
9YRC p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Deposited 2025-10-16	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain I 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å

179 other PDB entries and 217 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL40A_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–76

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8hte
Deposition date deposition_date	2022-12-21
Structure title title	Crystal structure of an effector mutant in complex with ubiquitin
Keywords keywords	Transferase, Ubiquitination; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.70 Å
Radius of gyration Rg (electron density) rg_electron	20.72 Å
Forward intensity I(0) i0	21198100.00
Molecular weight molecular_weight	33870.0 kDa
Excluded volume excluded_volume	41882 Å³
Envelope volume envelope_volume	50514 Å³
Hydration-shell volume shell_volume	20657 Å³
Envelope diameter envelope_diameter	69.6 Å
Shell Rg shell_rg	26.65 Å
Envelope Rg envelope_rg	20.67 Å
Shape Rg shape_rg	20.70 Å
Total Rg total_rg	21.55 Å
Total atoms total_atoms	2380
Residues n_residues	297
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	69.4 Å
Rg (real space) rg_real	21.65 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	2.1200e+07
I(0) uncertainty (real space) i0_real_error	3.0350e+05
Rg (reciprocal space) rg_reciprocal	21.66 Å
I(0) (reciprocal space) i0_reciprocal	21200000.0000
Solution quality estimate total_estimate	0.9005
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.275
Kurtosis Kurtosis kurtosis	-0.434
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5341000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	NAD(+)--protein-threonine ADP-ribosyltransferase
Molecular weight formula_weight	26020.9 kDa
EC 编号 ec_number	2.4.2.-
Mutation mutation	E220A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2639

SNRQEKLAQLMRQFESGGLYLRTVSDHRDEFENTFMPKLDACLGHGCDERYWSSATFIQQGLNGKVHDPHADRTGLIISADARLGGFSTFDAATANVPSGLEPSQYFPGQFPKFDMMGAYQATWNEDIFSVDATAVSEQQMDELGIPDEYRSVFDFDRIQEKMAQPRLAGREVEPTAAKICYQPKDVLGIYVDVDSPASQSKARELQQAMREQGFDLPFIAYRGGAAQELASV

来源 Source

来源生物 organism	Chromobacterium violaceum ATCC 12472
NCBI Class编号 ncbi_taxonomy_id	243365
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8568.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	NICOTINAMIDE
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ;
Molecular weight formula_weight	559.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	259

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8. Citations (1)

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Unit-cell length a length_a	59.074 Å
Unit-cell length b length_b	70.478 Å
Unit-cell length c length_c	90.562 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.307 Å
Low-resolution limit resolution_low	32.840 Å
R factor r_factor	0.1742
R_work r_work	0.1714
R_free r_free	0.2278

fit	/app/data/saxs_computation/ht/8hte/8hte.fit
pddf	/app/data/pr_computation/ht/8hte/8hte.pr.out
profile	/app/data/saxs_computation/ht/8hte/8hte.dat

Crystal structure of an effector mutant in complex with ubiquitin

1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD(+)--protein-threonine ADP-ribosyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)