40S ribosomal protein S5
OrganismNot specified
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein–RNA Heteromer Protein × 55 RNA 3 PDB declaration: 58-meric（58） Consistent with all polymer counts | Chain SG； UniProt 1–225 | Not recorded | U3 snoRNA × 1 ;5' ETS ; × 1 18S rRNA × 1 40S ribosomal protein S9-A × 1 （O13516） 40S ribosomal protein S12 × 1 （P48589） 40S ribosomal protein S13 × 1 （P05756） 40S ribosomal protein S14-A × 1 （P06367） 40S ribosomal protein S16-A × 1 （P0CX51） 40S ribosomal protein S18-A × 1 （P0CX55） 40S ribosomal protein S23-A × 1 （P0CX29） 40S ribosomal protein S28-A × 1 （Q3E7X9） ;rRNA 2'-O-methyltransferase fibrillarin ; × 2 （P15646） Nucleolar protein 56 × 1 （Q12460） Nucleolar protein 58 × 1 （Q12499） Ribosomal RNA-processing protein 9 × 1 （Q06506） 13 kDa ribonucleoprotein-associated protein × 2 （P39990） U3 small nucleolar RNA-associated protein 4 × 1 （Q06679） U3 small nucleolar RNA-associated protein 5 × 1 （Q04177） U3 small nucleolar RNA-associated protein 8 × 1 （P53276） U3 small nucleolar RNA-associated protein 9 × 1 （P38882） U3 small nucleolar RNA-associated protein 10 × 1 （P42945） U3 small nucleolar RNA-associated protein 15 × 1 （Q04305） NET1-associated nuclear protein 1 × 1 （Q02931） Periodic tryptophan protein 2 × 1 （P25635） U3 small nucleolar RNA-associated protein 12 × 1 （Q12220） U3 small nucleolar RNA-associated protein 13 × 1 （Q05946） U3 small nucleolar RNA-associated protein 18 × 1 （P40362） U3 small nucleolar RNA-associated protein 21 × 1 （Q06078） U3 small nucleolar RNA-associated protein 6 × 1 （Q02354） Bud site selection protein 21 × 1 （Q08492） U3 small nucleolar RNA-associated protein 7 × 1 （P40055） U3 small nucleolar RNA-associated protein 11 × 1 （P34247） U3 small nucleolar RNA-associated protein MPP10 × 1 （P47083） U3 small nucleolar ribonucleoprotein protein IMP3 × 1 （P32899） U3 small nucleolar ribonucleoprotein protein IMP4 × 1 （P53941） Something about silencing protein 10 × 1 （Q12136） Protein SOF1 × 1 （P33750） rRNA-processing protein FCF2 × 1 （Q12035） rRNA-processing protein FCF1 × 1 （Q05498） KRR1 small subunit processome component × 1 （P25586） rRNA biogenesis protein RRP5 × 1 （Q05022） U3 small nucleolar RNA-associated protein 22 × 1 （P53254） Ribosomal RNA-processing protein 7 × 1 （P25368） Ribosomal RNA small subunit methyltransferase NEP1 × 2 （Q06287） Ribosome biogenesis protein UTP30 × 1 （P36144） Ribosome biogenesis protein BMS1 × 1 （Q08965） ;RNA 3'-terminal phosphate cyclase-like protein ; × 1 （Q08096） Nucleolar complex protein 14 × 1 （Q99207） Nucleolar complex protein 4 × 1 （Q06512） U3 small nucleolar RNA-associated protein 14 × 1 （Q04500） Essential nuclear protein 1 × 1 （P38333） Pno1 × 1 Regulator of rDNA transcription protein 14 × 1 （P40470） Unassigned peptides 1 × 1 ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE | Resolution 4.60 Å |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 7D5S | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2NOQ Structure of ribosome-bound cricket paralysis virus IRES RNA Deposited 2006-10-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: octameric |
Chain F
75–224（150 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
20 mM Hepes pH 7.6, 100 mM KAc, 100 mM KCl, 5 mM MgCl2, 1 mM DTT, 1mM AEBSF, Roche Complete Protease Inhibitor；pH 7.6；20 mM Hepes pH 7.6, 100 mM KAc, 100 mM KCl, 5 mM MgCl2, 1 mM DTT, 1mM AEBSF, Roche Complete Protease Inhibitor
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.30 Å |
| 3J6X S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 5 degree rotation (Class II) Deposited 2014-04-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric |
Chain S5
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions
Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
|
Resolution 6.10 Å |
| 3J6Y S. cerevisiae 80S ribosome bound with Taura syndrome virus (TSV) IRES, 2 degree rotation (Class I) Deposited 2014-04-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric |
Chain S5
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin；pH 7.5；45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/uL RNasin
cryo-EM vitrification conditions
Fresh glow discharge, 7 second blot；Cryogen ETHANE；Fresh glow discharge, 7 second blot before plunging into liquid ehtane (FEI VITROBOT MARK II).
|
Resolution 6.10 Å |
| 3J77 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - rotated ribosome with 1 tRNA) Deposited 2014-05-29 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric |
Chain S5
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2；pH 7.5；20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK II)
|
Resolution 6.20 Å |
| 3J78 Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) Deposited 2014-05-29 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric |
Chain S5
1–225（225 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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å R-free 0.245 |
| 4U3M Crystal structure of Anisomycin bound to the yeast 80S ribosome Deposited 2014-07-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 ANM ANISOMYCIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å R-free 0.245 |
| 4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å R-free 0.237 |
| 4U3N Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome Deposited 2014-07-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å R-free 0.237 |
| 4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 2.90 Å R-free 0.245 |
| 4U3U Crystal structure of Cycloheximide bound to the yeast 80S ribosome Deposited 2014-07-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 2.90 Å R-free 0.245 |
| 4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 EDE EDEINE B × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å R-free 0.252 |
| 4U4N Crystal structure of Edeine bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 EDE EDEINE B × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å R-free 0.252 |
| 4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 GET GENETICIN × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.60 Å R-free 0.267 |
| 4U4O Crystal structure of Geneticin bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.60 Å R-free 0.267 |
| 4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å R-free 0.255 |
| 4U4Q Crystal structure of Homoharringtonine bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å R-free 0.255 |
| 4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 2.80 Å R-free 0.246 |
| 4U4R Crystal structure of Lactimidomycin bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 2.80 Å R-free 0.246 |
| 4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å R-free 0.259 |
| 4U4U Crystal structure of Lycorine bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 733 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3KD (1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å R-free 0.259 |
| 4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 PCY Pactamycin × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å R-free 0.245 |
| 4U4Y Crystal structure of Pactamycin bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 PCY Pactamycin × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å R-free 0.245 |
| 4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 677 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å R-free 0.252 |
| 4U4Z Crystal structure of Phyllanthoside bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 95-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3K5 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å R-free 0.252 |
| 4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å R-free 0.262 |
| 4U50 Crystal structure of Verrucarin bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 576 ZN ZINC ION × 8 3L2 (4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å R-free 0.262 |
| 4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å R-free 0.253 |
| 4U51 Crystal structure of Narciclasine bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 572 ZN ZINC ION × 8 3KF (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å R-free 0.253 |
| 4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 679 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J2 Nagilactone C × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å R-free 0.258 |
| 4U52 Crystal structure of Nagilactone C bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 734 OHX osmium (III) hexammine × 575 ZN ZINC ION × 8 3J2 Nagilactone C × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.00 Å R-free 0.258 |
| 4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 676 OHX osmium (III) hexammine × 556 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.30 Å R-free 0.255 |
| 4U53 Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 730 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 3J6 (3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.30 Å R-free 0.255 |
| 4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å R-free 0.246 |
| 4U55 Crystal structure of Cryptopleurine bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-MERIC |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 3K8 (14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.20 Å R-free 0.246 |
| 4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 675 OHX osmium (III) hexammine × 558 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.45 Å R-free 0.260 |
| 4U56 Crystal structure of Blasticidin S bound to the yeast 80S ribosome Deposited 2014-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 732 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 BLS BLASTICIDIN S × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.45 Å R-free 0.260 |
| 4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 678 OHX osmium (III) hexammine × 557 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å R-free 0.247 |
| 4U6F Crystal structure of T-2 toxin bound to the yeast 80S ribosome Deposited 2014-07-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 731 OHX osmium (III) hexammine × 574 ZN ZINC ION × 8 ZBA 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å R-free 0.247 |
| 4V4B Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map. Deposited 2004-01-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric |
Chain AG
75–224（150 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM vitrification conditions
Cryogen ETHANE；Rapid-freezing in liquid ethane
|
Resolution 11.70 Å |
| 4V6I Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome Deposited 2010-10-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric |
Chain AF
1–225（225 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 |
| 4V7R Yeast 80S ribosome. Deposited 2010-07-23 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 73-meric |
Chain AD
1–225（225 aa）
|
Not recorded | OHX osmium (III) hexammine × 355 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
|
Resolution 4.00 Å R-free 0.341 |
| 4V7R Yeast 80S ribosome. Deposited 2010-07-23 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric |
Chain CD
1–225（225 aa）
|
Not recorded | OHX osmium (III) hexammine × 360 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；297 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K
|
Resolution 4.00 Å R-free 0.341 |
| 4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain AF
1–225（225 aa）
|
Not recorded | OHX osmium (III) hexammine × 657 MG MAGNESIUM ION × 1035 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.00 Å R-free 0.229 |
| 4V88 The structure of the eukaryotic ribosome at 3.0 A resolution. Deposited 2011-10-11 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain CF
1–225（225 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 |
| 4V8Y Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex Deposited 2013-07-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric |
Chain AF
1–225（225 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 79 PDB declaration: 85-meric |
Chain AF
1–225（225 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 |
| 5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-MERIC |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 580 OHX osmium (III) hexammine × 601 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.15 Å R-free 0.252 |
| 5DAT Complex of yeast 80S ribosome with hypusine-containing eIF5A Deposited 2015-08-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 86-MERIC |
Chain S5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 528 OHX osmium (III) hexammine × 565 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.15 Å R-free 0.252 |
| 5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric |
Chain S5
2–225（224 aa）
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.25 Å R-free 0.301 |
| 5DC3 Complex of yeast 80S ribosome with non-modified eIF5A Deposited 2015-08-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: 81-meric |
Chain s5
2–225（224 aa）
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.25 Å R-free 0.301 |
| 5DGE Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome Deposited 2015-08-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 155 PDB declaration: 165-meric |
Chain S5
2–225（224 aa）
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 1093 OHX osmium (III) hexammine × 1169 ZN ZINC ION × 16 SPS SPARSOMYCIN × 2 PRO PROLINE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.45 Å R-free 0.263 |
| 5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: TRIMERIC |
Chain S5
2–225（224 aa）
|
Not recorded | ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 4 OHX osmium (III) hexammine × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.30 Å R-free 0.310 |
| 5DGF Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 80 PDB declaration: TRIMERIC |
Chain s5
2–225（224 aa）
|
Not recorded | ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 8 OHX osmium (III) hexammine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.30 Å R-free 0.310 |
| 5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 81-MERIC |
Chain s5
2–225（224 aa）
|
Not recorded | ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.10 Å R-free 0.284 |
| 5DGV Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog Deposited 2015-08-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-MERIC |
Chain S5
2–225（224 aa）
|
Not recorded | ZN ZINC ION × 8 SPS SPARSOMYCIN × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.10 Å R-free 0.284 |
| 5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 aa）
|
Not recorded | OHX osmium (III) hexammine × 874 MG MAGNESIUM ION × 994 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
|
Resolution 3.40 Å R-free 0.284 |
| 5FCI Structure of the vacant uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
2–225（224 aa）
|
Not recorded | OHX osmium (III) hexammine × 561 MG MAGNESIUM ION × 626 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-Acetate pH 7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
|
Resolution 3.40 Å R-free 0.284 |
| 5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric |
Chain s5
2–225（224 aa）
|
Not recorded | MG MAGNESIUM ION × 517 OHX osmium (III) hexammine × 534 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000
|
Resolution 3.10 Å R-free 0.291 |
| 5FCJ Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome Deposited 2015-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
2–225（224 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 |
| 5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
20–225（206 aa）
|
Not recorded | OHX osmium (III) hexammine × 481 MG MAGNESIUM ION × 493 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å R-free 0.251 |
| 5I4L Crystal structure of Amicoumacin A bound to the yeast 80S ribosome Deposited 2016-02-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain s5
20–225（206 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric |
Chain CB
1–225（225 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 5JUP Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit) Deposited 2016-05-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric |
Chain CB
1–225（225 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 5JUS Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure III (mid-rotated 40S subunit) Deposited 2016-05-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric |
Chain CB
1–225（225 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
|
Resolution 4.20 Å |
| 5JUT Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit) Deposited 2016-05-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric |
Chain CB
1–225（225 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 5JUU Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure V (least rotated 40S subunit) Deposited 2016-05-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric |
Chain CB
1–225（225 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric |
Chain S5
20–225（206 aa）
|
Not recorded | MG MAGNESIUM ION × 1026 OHX osmium (III) hexammine × 659 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；277 K；Tris-Acetate pH 7.0, KSCN, MgOAc2, glycerol, spermidine, PEG20K
|
Resolution 3.25 Å R-free 0.249 |
| 5LYB Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn Deposited 2016-09-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric |
Chain s5
20–225（206 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 conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric |
Chain F2
20–225（206 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1058 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5CR N-acetyl-L-phenylalanine × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 5MC6 Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Deposited 2016-11-09 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric |
Chain B
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric |
Chain G
20–225（206 aa）
|
Not recorded | OHX osmium (III) hexammine × 517 MG MAGNESIUM ION × 673 7MB Agelastatin A × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.50 Å R-free 0.239 |
| 5MEI Crystal structure of Agelastatin A bound to the 80S ribosome Deposited 2016-11-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric |
Chain s5
20–225（206 aa）
|
Not recorded | OHX osmium (III) hexammine × 553 MG MAGNESIUM ION × 733 7MB Agelastatin A × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.50 Å R-free 0.239 |
| 5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
20–225（206 aa）
|
Not recorded | MG MAGNESIUM ION × 597 GET GENETICIN × 9 ZN ZINC ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.70 Å R-free 0.253 |
| 5NDG Crystal structure of geneticin (G418) bound to the yeast 80S ribosome Deposited 2017-03-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric |
Chain s5
20–225（206 aa）
|
Not recorded | MG MAGNESIUM ION × 624 GET GENETICIN × 12 ZN ZINC ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.70 Å R-free 0.253 |
| 5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric |
Chain s5
20–225（206 aa）
|
Not recorded | PAR PAROMOMYCIN × 40 MG MAGNESIUM ION × 1006 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.30 Å R-free 0.250 |
| 5NDV Crystal structure of Paromomycin bound to the yeast 80S ribosome Deposited 2017-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric |
Chain S5
20–225（206 aa）
|
Not recorded | PAR PAROMOMYCIN × 47 MG MAGNESIUM ION × 1133 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.30 Å R-free 0.250 |
| 5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain s5
20–225（206 aa）
|
Not recorded | MG MAGNESIUM ION × 671 8UZ TC007 × 10 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.70 Å R-free 0.235 |
| 5NDW Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome Deposited 2017-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain S5
20–225（206 aa）
|
Not recorded | MG MAGNESIUM ION × 694 8UZ TC007 × 15 ZN ZINC ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.70 Å R-free 0.235 |
| 5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-MERIC |
Chain S5
20–225（206 aa）
|
Not recorded | MG MAGNESIUM ION × 855 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 22 ZN ZINC ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.40 Å R-free 0.238 |
| 5OBM Crystal structure of Gentamicin bound to the yeast 80S ribosome Deposited 2017-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-MERIC |
Chain s5
20–225（206 aa）
|
Not recorded | MG MAGNESIUM ION × 1211 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 47 ZN ZINC ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.40 Å R-free 0.238 |
| 5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 78-meric |
Chain G
20–225（206 aa）
|
Not recorded | OHX osmium (III) hexammine × 515 MG MAGNESIUM ION × 703 HN8 Haemanthamine × 1 GOL GLYCEROL × 2 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å R-free 0.252 |
| 5ON6 Crystal structure of haemanthamine bound to the 80S ribosome Deposited 2017-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 77 PDB declaration: 80-meric |
Chain s5
20–225（206 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 |
| 5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain G
20–225（206 aa）
|
Not recorded | OHX osmium (III) hexammine × 518 MG MAGNESIUM ION × 666 7AL Chlorolissoclimide × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；Tris-acetate pH7.0, potassium thiocyanate, magnesium acetate, glycerol, spermidine, PEG 20000
|
Resolution 3.00 Å R-free 0.227 |
| 5TBW Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome Deposited 2016-09-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric |
Chain s5
20–225（206 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 |
| 5TGM Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro Deposited 2016-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 164-meric |
Chain S5
20–225（206 aa）
Chain s5
20–225（206 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 |
| 5TZS Architecture of the yeast small subunit processome Deposited 2016-11-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain 6
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.7
cryo-EM vitrification conditions
Cryogen ETHANE；Incubated 10 seconds on the grid before blotting (blot time 2.0 seconds, blot force 0) and freezing.
|
Resolution 5.10 Å |
| 5WYJ Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1) Deposited 2017-01-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 64-meric |
Chain SG
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.70 Å |
| 5WYK Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP) Deposited 2017-01-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric |
Chain SG
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2 seconds before plunging
|
Resolution 4.50 Å |
| 6EML Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae Deposited 2017-10-02 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 31-meric |
Chain B
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 6FAI Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit Deposited 2017-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric |
Chain F
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 46 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.40 Å |
| 6GQ1 Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) Deposited 2018-06-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric |
Chain v
20–225（206 aa）
|
Not recorded | ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot force 4, blot waiting time 30 s
|
Resolution 4.40 Å |
| 6GQB Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) Deposited 2018-06-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric |
Chain v
20–225（206 aa）
|
Not recorded | ZN ZINC ION × 8 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot force 4, blot waiting time 30 s
|
Resolution 3.90 Å |
| 6GQV Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) Deposited 2018-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric |
Chain v
20–225（206 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 |
| 6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain G
1–225（225 aa）
|
Not recorded | OHX osmium (III) hexammine × 513 MG MAGNESIUM ION × 717 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å R-free 0.264 |
| 6HHQ Crystal structure of compound C45 bound to the yeast 80S ribosome Deposited 2018-08-28 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric |
Chain s5
1–225（225 aa）
|
Not recorded | OHX osmium (III) hexammine × 544 MG MAGNESIUM ION × 792 G5B (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
|
Resolution 3.10 Å R-free 0.264 |
| 6I7O The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition. Deposited 2018-11-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 163-meric |
Chain B
20–225（206 aa）
Chain Bb
20–225（206 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 |
| 6KE6 3.4 angstrom cryo-EM structure of yeast 90S small subunit preribosome Deposited 2019-07-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric |
Chain SG
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；wait 30s and blot 2s before plunging
|
Resolution 3.40 Å |
| 6LQP Cryo-EM structure of 90S small subunit preribosomes in transition states (State A) Deposited 2020-01-14 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 73-meric |
Chain SG
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 6LQQ Cryo-EM structure of 90S small subunit preribosomes in transition states (State B) Deposited 2020-01-14 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 67 PDB declaration: 70-meric |
Chain SG
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6LQR Cryo-EM structure of 90S small subunit preribosomes in transition states (State C) Deposited 2020-01-14 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 68-meric |
Chain SG
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.60 Å |
| 6LQS Cryo-EM structure of 90S small subunit preribosomes in transition states (State D) Deposited 2020-01-14 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 79-meric |
Chain SG
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6LQT Cryo-EM structure of 90S small subunit preribosomes in transition states (State E) Deposited 2020-01-14 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric |
Chain SG
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.90 Å |
| 6LQU Cryo-EM structure of 90S small subunit preribosomes in transition states (State A1) Deposited 2020-01-14 | Different oligomeric state Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric |
Chain SG
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6LQV Cryo-EM structure of 90S small subunit preribosomes in transition states (State C1) Deposited 2020-01-14 | Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric |
Chain SG
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 6RBD State 1 of yeast Tsr1-TAP Rps20-Deltaloop pre-40S particles Deposited 2019-04-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 35-meric |
Chain F
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot 1.7-1.9 seconds before plunging
|
Resolution 3.47 Å |
| 6RBE State 2 of yeast Tsr1-TAP Rps20-Deltaloop pre-40S particles Deposited 2019-04-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 33-meric |
Chain F
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot 1.7-1.9 seconds before plunging
|
Resolution 3.80 Å |
| 6SNT Yeast 80S ribosome stalled on SDD1 mRNA. Deposited 2019-08-27 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric |
Chain F
1–225（225 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 |
| 6WDR Subunit joining exposes nascent pre-40S rRNA for processing and quality control Deposited 2020-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 32-meric |
Chain F
20–225（206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6Y7C Early cytoplasmic yeast pre-40S particle (purified with Tsr1 as bait) Deposited 2020-02-28 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric |
Chain F
1–225（225 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 |
| 6Z6J Cryo-EM structure of yeast Lso2 bound to 80S ribosomes under native condition Deposited 2020-05-28 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain SF
1–225（225 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 |
| 6ZCE Structure of a yeast ABCE1-bound 43S pre-initiation complex Deposited 2020-06-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 45-meric |
Chain G
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.30 Å |
| 6ZQA Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state A (Poly-Ala) Deposited 2020-07-09 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric |
Chain DF
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 6ZQB Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state B2 Deposited 2020-07-09 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric |
Chain DF
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6ZQC Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Pre-A1 Deposited 2020-07-09 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric |
Chain DF
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6ZQE Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-A (Poly-Ala) Deposited 2020-07-09 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 62-meric |
Chain DF
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.10 Å |
| 6ZQF Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-B (Poly-Ala) Deposited 2020-07-09 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric |
Chain DF
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.90 Å |
| 6ZQG Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-C Deposited 2020-07-09 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric |
Chain DF
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7A1G Structure of a crosslinked yeast ABCE1-bound 43S pre-initiation complex Deposited 2020-08-13 | Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric |
Chain B
20–225（206 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7AJT Cryo-EM structure of the 90S-exosome super-complex (state Pre-A1-exosome) Deposited 2020-09-29 | Different oligomeric state Different ligand/ion | Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric |
Chain DF
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 3 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 7AJU Cryo-EM structure of the 90S-exosome super-complex (state Post-A1-exosome) Deposited 2020-09-29 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric |
Chain DF
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7B7D Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Deposited 2020-12-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric |
Chain B
20–225（206 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 |
| 7D4I Cryo-EM structure of 90S small ribosomal precursors complex with the DEAH-box RNA helicase Dhr1 (State F) Deposited 2020-09-24 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric |
Chain SG
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7D5T Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1) Deposited 2020-09-28 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric |
Chain SG
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.00 Å |
| 7D63 Cryo-EM structure of 90S preribosome with inactive Utp24 (state C) Deposited 2020-09-29 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric |
Chain SG
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 12.30 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 conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain BF
20–225（206 aa）
|
Not recorded | MG MAGNESIUM ION × 366 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å |
| 7MPJ Stm1 bound vacant 80S structure isolated from wild-type Deposited 2021-05-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain BF
20–225（206 aa）
|
Not recorded | MG MAGNESIUM ION × 745 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 7N8B Cycloheximide bound vacant 80S structure isolated from cbf5-D95A Deposited 2021-06-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain BF
20–225（206 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 conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric |
Chain SB
20–225（206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.90 Å |
| 7NRD Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA Deposited 2021-03-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric |
Chain SB
20–225（206 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 |
| 7SUK Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Processome Isolated from R2TP-depleted Yeast Cells Deposited 2021-11-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 67 PDB declaration: 70-meric |
Chain L5
13–225（213 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.99 Å |
| 7ZUX Collided ribosome in a disome unit from S. cerevisiae Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric |
Chain DF
20–225（206 aa）
|
Not recorded | MG MAGNESIUM ION × 86 ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 7ZW0 FAP-80S Complex - Rotated state Deposited 2022-05-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric |
Chain sB
1–225（225 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 |
| 8BQX Yeast 80S ribosome in complex with Map1 (conformation 2) Deposited 2022-11-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric |
Chain B
20–225（206 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 |
| 8C00 Enp1TAP-S21_A population of yeast small ribosomal subunit precursors depleted of rpS21/eS21 Deposited 2022-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 25 PDB declaration: 26-meric |
Chain B
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8C01 Enp1TAP_A population of yeast small ribosomal subunit precursors Deposited 2022-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 31-meric |
Chain B
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 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 conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 48-meric |
Chain B
1–225（225 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 conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric |
Chain C
1–225（225 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 |
| 8CBJ Cryo-EM structure of Otu2-bound cytoplasmic pre-40S ribosome biogenesis complex Deposited 2023-01-25 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 39-meric |
Chain F
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 46 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8CCS 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex Deposited 2023-01-27 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric |
Chain i
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 281 K POTASSIUM ION × 22 SPD SPERMIDINE × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.97 Å |
| 8CDL 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex Deposited 2023-01-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric |
Chain i
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 258 K POTASSIUM ION × 21 SPD SPERMIDINE × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.72 Å |
| 8CDR Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-01-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric |
Chain i
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 267 SPD SPERMIDINE × 4 K POTASSIUM ION × 21 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.04 Å |
| 8CEH Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-01 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric |
Chain i
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 262 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.05 Å |
| 8CF5 Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-02 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric |
Chain i
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 241 K POTASSIUM ION × 21 SPD SPERMIDINE × 11 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.71 Å |
| 8CG8 Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric |
Chain i
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 241 SPD SPERMIDINE × 8 K POTASSIUM ION × 19 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.57 Å |
| 8CGN Non-rotated 80S S. cerevisiae ribosome with ligands Deposited 2023-02-06 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric |
Chain i
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 263 K POTASSIUM ION × 19 SPD SPERMIDINE × 4 MET METHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.28 Å |
| 8CIV Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin Deposited 2023-02-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric |
Chain i
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 251 K POTASSIUM ION × 21 SPD SPERMIDINE × 3 SO1 [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.47 Å |
| 8CKU Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin Deposited 2023-02-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric |
Chain i
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 205 K POTASSIUM ION × 16 SPD SPERMIDINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.11 Å |
| 8CMJ Translocation intermediate 4 (TI-4*) of 80S S. cerevisiae ribosome with eEF2 in the absence of sordarin Deposited 2023-02-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric |
Chain i
1–225（225 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 |
| 8K2D Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A Deposited 2023-07-12 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric |
Chain SF
1–225（225 aa）
|
Not recorded | ZN ZINC ION × 9 T1C TIGECYCLINE × 6 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8K82 Cryo-EM structure of the yeast 80S ribosome with tigecycline, Not5 and P-site tRNA Deposited 2023-07-28 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric |
Chain SF
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 316 T1C TIGECYCLINE × 6 SPD SPERMIDINE × 1 ZN ZINC ION × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain G
1–225（225 aa）
|
Not recorded | OHX osmium (III) hexammine × 461 MG MAGNESIUM ION × 711 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 8 OS OSMIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
|
Resolution 3.16 Å R-free 0.251 |
| 8P4V 80S yeast ribosome in complex with HaterumaimideQ Deposited 2023-05-23 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric |
Chain s5
1–225（225 aa）
|
Not recorded | OHX osmium (III) hexammine × 492 MG MAGNESIUM ION × 766 K POTASSIUM ION × 5 SPD SPERMIDINE × 1 X1K (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 ZN ZINC ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
|
Resolution 3.16 Å R-free 0.251 |
| 8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric |
Chain G
1–225（225 aa）
|
Not recorded | OHX osmium (III) hexammine × 484 MG MAGNESIUM ION × 717 K POTASSIUM ION × 2 SPD SPERMIDINE × 1 VDU fluorolissoclimide × 1 ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
|
Resolution 2.90 Å R-free 0.223 |
| 8P85 80S yeast ribosome in complex with Fluorolissoclimide Deposited 2023-08-31 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric |
Chain s5
1–225（225 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 |
| 8P9A 80S yeast ribosome in complex with Methyllissoclimide Deposited 2023-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 150 PDB declaration: 158-meric |
Chain G
1–225（225 aa）
Chain s5
1–225（225 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 |
| 8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric |
Chain G
1–225（225 aa）
|
Not recorded | OHX osmium (III) hexammine × 456 MG MAGNESIUM ION × 707 ZN ZINC ION × 8 K POTASSIUM ION × 1 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
|
Resolution 2.90 Å R-free 0.230 |
| 8PNN 80S yeast ribosome in complex with Bromolissoclimide Deposited 2023-06-30 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric |
Chain s5
1–225（225 aa）
|
Not recorded | OHX osmium (III) hexammine × 479 MG MAGNESIUM ION × 783 ZN ZINC ION × 7 K POTASSIUM ION × 3 ZWB (3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~{a}-trimethyl-2-methylidene-3-oxidanyl-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione × 1 SPD SPERMIDINE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion
|
Resolution 2.90 Å R-free 0.230 |
| 8UT0 Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA Deposited 2023-10-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric |
Chain SB
20–225（206 aa）
|
Not recorded | 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.22 Å |
| 8UTI Eukaryotic 80S ribosome with Reh1 and A/P site tRNA Deposited 2023-10-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric |
Chain SB
20–225（206 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 conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric |
Chain SB
20–225（206 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 |
| 8YLD State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation Deposited 2024-03-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric |
Chain SB
20–225（206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8YLR State 6 (S6) of yeast 80S ribosome bound to 2 tRNAs and eEF2 and eEF3 during tranlocation Deposited 2024-03-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric |
Chain SB
20–225（206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8Z70 State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding Deposited 2024-04-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric |
Chain SB
20–225（206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8Z71 State 1a (S1a) of yeast 80S ribosome bound to open eEF3 and 2 tRNAs and eEF1A during mRNA decoding Deposited 2024-04-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric |
Chain SB
20–225（206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8ZGR 80S ribosome with A/A tRNA and mRNA of WNV Deposited 2024-05-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 79-meric |
Chain SB
20–225（206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8ZGY 80S ribosome with P/E tRNA and mRNA of WNV Deposited 2024-05-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric |
Chain SB
20–225（206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8ZH3 80S ribosome with A/P-P/E tRNA and mRNA of WNV Deposited 2024-05-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric |
Chain SB
20–225（206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8ZHB 80S ribosome with A/A P/E tRNA and mRNA of WNV Deposited 2024-05-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 81-meric |
Chain SB
20–225（206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8ZHC pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV Deposited 2024-05-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric |
Chain SB
20–225（206 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 |
| 9F9S Yeast SDD1 Disome with Mbf1 Deposited 2024-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 152 PDB declaration: 164-meric |
Chain Rf
1–225（225 aa）
Chain Sf
1–225（225 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 |
| 9G33 Stalled 90S - Utp23-Krr1-deltaC3 Deposited 2024-07-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 62 PDB declaration: 65-meric |
Chain DF
1–225（225 aa）
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å |
| 9N6V SSU processome maturation and disassembly, State A Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric |
Chain L5
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 25 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 9N6W SSU processome maturation and disassembly, State A* Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric |
Chain L5
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 25 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å |
| 9N6X SSU processome maturation and disassembly, State B Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric |
Chain L5
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 34 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.71 Å |
| 9N6Y SSU processome maturation and disassembly, State C Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 73-meric |
Chain L5
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 34 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.65 Å |
| 9N6Z SSU processome maturation and disassembly, State D Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric |
Chain L5
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.74 Å |
| 9N70 SSU processome maturation and disassembly, State E Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric |
Chain L5
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.17 Å |
| 9N72 SSU processome maturation and disassembly, State F Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 73-meric |
Chain L5
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.94 Å |
| 9N73 SSU processome maturation and disassembly, State G Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 71 PDB declaration: 74-meric |
Chain L5
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.96 Å |
| 9N74 SSU processome maturation and disassembly, State H Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric |
Chain L5
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 39 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.65 Å |
| 9N75 SSU processome maturation and disassembly, State I Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 68-meric |
Chain L5
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 59 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 9N76 SSU processome maturation and disassembly, State J Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 67-meric |
Chain L5
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 38 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 9N77 SSU processome maturation and disassembly, State K Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 64-meric |
Chain L5
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 48 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.94 Å |
| 9N78 SSU processome maturation and disassembly, State L Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 59-meric |
Chain L5
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.17 Å |
| 9N79 SSU processome maturation and disassembly, State M Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric |
Chain L5
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.93 Å |
| 9N7A SSU processome maturation and disassembly, State N Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 39-meric |
Chain L5
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.84 Å |
| 9N7B SSU processome maturation and disassembly, State O Deposited 2025-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric |
Chain L5
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 9PN5 Composite map of hypomethylated 80S ribosome treated with hygromycin B Deposited 2025-07-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric |
Chain BF
1–225（225 aa）
|
Not recorded | MG MAGNESIUM ION × 174 K POTASSIUM ION × 27 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.75 Å |
| 9R9O Yeast 80S with nascent chain in complex with Ssb1-ADP in the S1 state Deposited 2025-05-20 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric |
Chain SF
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9R9P Yeast 80S with nascent chain in complex with Ssb1-ADP in the S2 state Deposited 2025-05-20 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric |
Chain SF
1–225（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
153 other PDB entries and 191 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | RS5_YEAST |
| Isoform | — |
| PDB entities | 4 |
| Chains and sequence ranges | Author chain SG； PDBConstruct 1–225； UniProt 1–225 |
