← Back to search
4rf0

Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease in complex with ubiquitin (space group P6522)

Method: X-RAY DIFFRACTION Dmax: 82.8 Å Quality: REASONABLE
▼

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

ORF1ab protein

Human betacoronavirus 2c Jordan-N3/2012

UniProt M4STU1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1480–1803 Fragment：UNP residues 1480-1803 Ubiquitin-60S ribosomal protein L40 × 1 （P62987） ZN ZINC ION × 1 SO4 SULFATE ION × 9 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；1.80 M ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.80 Å R-free 0.281

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 4RF0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4REZ Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease Deposited 2014-09-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1480–1803（324 aa） Fragment：UNP residues 1480-1803
Not recorded ZN ZINC ION × 1 PGO S-1,2-PROPANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；18% PEG 4000, 0.1 M trisodium citrate, 16% isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.274
4RF1 Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease in complex with ubiquitin (space group P63) Deposited 2014-09-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1480–1803（324 aa） Fragment：UNP residues 1480-1803
Not recorded ZN ZINC ION × 1 PGO S-1,2-PROPANEDIOL × 5 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；20% PEG 4000, 0.1 M trisodium citrate, 20% isopropanol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.15 Å R-free 0.231

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

View Construct and Data Evidence
UniProt name M4STU1_9BETC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–324； UniProt 1480–1803

Ubiquitin-60S ribosomal protein L40

Homo sapiens

UniProt P62987

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–75 Fragment：UNP residues 1-75 ORF1ab protein × 1 （M4STU1） ZN ZINC ION × 1 SO4 SULFATE ION × 9 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；1.80 M ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.80 Å R-free 0.281

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 4RF0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
11TA Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused) Deposited 2026-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain I 1–76（76 aa）
Chain K 1–76（76 aa）
Not recorded ZN ZINC ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；50 mM HEPES, pH 7.6, 150 mM KCl, 5 mM MgCl2, 2 mM ATP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
22TU Human 80S ribosome in complex with DHX29 Deposited 2026-01-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
28LN XBP1u-stalled RPL4 RNC in complex with NAC Deposited 2026-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain Bm 1–128（128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.70 Å
2LJ5 Description of the Structural fluctuations of proteins from structure-based calculations of Residual dipolar couplings Deposited 2011-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；300 K；Ionic strength (raw mmCIF value) 200；Pressure ambient
NMR sample composition 200 mM protein, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MJB Solution nmr structure of ubiquitin refined against dipolar couplings in 4 media Deposited 2014-01-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 229–304（76 aa） Fragment：Ubiquitin-like 3 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；308 K；Pressure ambient
NMR measurement conditions pH 6；298 K；Pressure ambient
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N; U-100% 2H] ubiquitin, 20 mM [U-100% 2H] D4-imidazole, 4.8 mM squalamine, 1.5 mM hexanol, 10 mM sodium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N; U-100% 2H] ubiquitin, 20 mM [U-100% 2H] D4-imidazole, 1.5 mM hexanol, 10 mM sodium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] ubiquitin, 13 mg/mL Pf1 phage, 140 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N; U-100% 2H] ubiquitin, 14 mg/mL Pf1 phage, 150 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2MUR Solution Structure of the Human FAAP20 UBZ-Ubiquitin Complex Deposited 2014-09-16 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 2 mM UBZ, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] UBZ, 0.8 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 3 mM [U-100% 13C; U-100% 15N] UBZ, 100% D2O | 100% D2O
NMR sample composition 3 mM Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 3 mM [U-100% 13C; U-100% 15N] UBZ, 100% D2O | 100% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 3 mM UBZ, 100% D2O | 100% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 2 mM UBZ, 100% D2O | 100% D2O
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] UBZ, 0.8 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM sodium phosphate, 100 mM potassium chloride, 100% D2O | 100% D2O
Resolution not provided
2N3U Solution structure of the Rpn1 T1 site engaging two monoubiquitin molecules Deposited 2015-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.6 mM [U-100% 15N] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.5 mM protein_1, 0.5 mM [U-100% 15N] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.6 mM [U-13C] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.6 mM protein_1, 0.6 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
2N3V Solution structure of the Rpn1 T1 site with K48-linked diubiquitin in the extended binding mode Deposited 2015-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 50；Pressure AMBIENT
NMR sample composition 0.3 MM [U-100% 15N] PROTEIN_1, 0.04-1.2 MM PROTEIN_2, 50 MM HEPES, 50 MM SODIUM CHLORIDE, 1 MM EDTA, 2 MM DTT, 0.1 % SODIUM AZIDE, 95% H2O/5% D2O
NMR sample composition 0.08-0.3 MM PROTEIN_1, 0.3 MM [U-100% 15N] PROTEIN_2, 50 MM HEPES, 50 MM SODIUM CHLORIDE, 1 MM EDTA, 2 MM DTT, 0.1 % SODIUM AZIDE, 95% H2O/ 5% D2O
NMR sample composition 0.06-0.5 MM PROTEIN_1, 0.5 MM [U-13C] PROTEIN_2, 50 MM HEPES, 50 MM SODIUM CHLORIDE, 1 MM EDTA, 2 MM DTT, 0.1 % SODIUM AZIDE, 100% D2O
NMR sample composition 0.6 MM [U-13C] PROTEIN_1, 0.6 MM PROTEIN_2, 50 MM HEPES, 50 MM SODIUM CHLORIDE, 1 MM EDTA, 2 MM DTT, 0.1 % SODIUM AZIDE, 100% D2O
NMR sample composition 0.5 MM PROTEIN_ 1, 0.5 MM [U-13C] PROTEIN_2, 50 MM HEPES, 50 MM SODIUM CHLORIDE, 1 MM EDTA, 2 MM DTT, 0.1 % SODIUM AZIDE, 100% D2O
NMR sample composition 0.6 MM [U-13C] PROTEIN_1, 0.12-0.6 MM PROTEIN_2, 50 MM HEPES, 50 MM SODIUM CHLORIDE, 1 MM EDTA, 2 MM DTT, 0.1 % SODIUM AZIDE, 100% D2O
Resolution not provided
2N3W Solution structure of the Rpn1 T1 site with K48-linked diubiquitin in the contracted binding mode Deposited 2015-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.3 mM [U-100% 15N] protein_1, 0.04-1.2 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.08-0.3 mM protein_1, 0.3 mM [U-100% 15N] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.06-0.5 mM protein_1, 0.5 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.6 mM [U-13C] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.5 mM protein_1, 0.5 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.6 mM [U-13C] protein_1, 0.12-0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
4JIO Bro1 V domain and ubiquitin Deposited 2013-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain U 1–76（76 aa）
Mutation：A28M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1 M bis-Tris propane pH 7, 0.2-0.4 M sodium malonate, 15-20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.60 Å R-free 0.421
4P4H Caught-in-action signaling complex of RIG-I 2CARD domain and MAVS CARD domain Deposited 2014-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric
Chain S 1–76（76 aa）
Chain T 1–76（76 aa）
Chain U 1–76（76 aa）
Chain W 1–76（76 aa）
Chain X 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Tri-Li Citrate, PEG 3350, Cr(III) Cl3
Resolution 3.40 Å R-free 0.240
4PIG Crystal structure of the ubiquitin K11S mutant Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：K11S CA CALCIUM ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M CaCl2, 0.1 M HEPES, 30% PEG 4000
Resolution 1.95 Å R-free 0.217
4PIG Crystal structure of the ubiquitin K11S mutant Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：K11S CA CALCIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M CaCl2, 0.1 M HEPES, 30% PEG 4000
Resolution 1.95 Å R-free 0.217
4PIG Crystal structure of the ubiquitin K11S mutant Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Mutation：K11S CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M CaCl2, 0.1 M HEPES, 30% PEG 4000
Resolution 1.95 Å R-free 0.217
4PIG Crystal structure of the ubiquitin K11S mutant Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–76（76 aa）
Mutation：K11S CA CALCIUM ION × 2 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M CaCl2, 0.1 M HEPES, 30% PEG 4000
Resolution 1.95 Å R-free 0.217
4PIG Crystal structure of the ubiquitin K11S mutant Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Mutation：K11S Mutation：K11S Mutation：K11S Mutation：K11S CA CALCIUM ION × 4 CL CHLORIDE ION × 8 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M CaCl2, 0.1 M HEPES, 30% PEG 4000
Resolution 1.95 Å R-free 0.217
4PIH X-ray crystal structure of the K33S mutant of ubiquitin Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：K33S CA CALCIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2M CaCl2, 0.1 M TRIS, 25% PEG 4000
Resolution 1.50 Å R-free 0.190
4PIH X-ray crystal structure of the K33S mutant of ubiquitin Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：K33S CA CALCIUM ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2M CaCl2, 0.1 M TRIS, 25% PEG 4000
Resolution 1.50 Å R-free 0.190
4PIH X-ray crystal structure of the K33S mutant of ubiquitin Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：K33S Mutation：K33S CA CALCIUM ION × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2M CaCl2, 0.1 M TRIS, 25% PEG 4000
Resolution 1.50 Å R-free 0.190
4PIH X-ray crystal structure of the K33S mutant of ubiquitin Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：K33S Mutation：K33S CA CALCIUM ION × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2M CaCl2, 0.1 M TRIS, 25% PEG 4000
Resolution 1.50 Å R-free 0.190
4PIJ X-ray crystal structure of the K11S/K63S double mutant of ubiquitin Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–75（75 aa）
Mutation：K11S, K63S GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0.2M ammonium sulfate, 25% PEG 4000
Resolution 1.50 Å R-free 0.198
4PIJ X-ray crystal structure of the K11S/K63S double mutant of ubiquitin Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–75（75 aa）
Mutation：K11S, K63S SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0.2M ammonium sulfate, 25% PEG 4000
Resolution 1.50 Å R-free 0.198
4PIJ X-ray crystal structure of the K11S/K63S double mutant of ubiquitin Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–75（75 aa）
Chain B 1–75（75 aa）
Mutation：K11S, K63S Mutation：K11S, K63S GOL GLYCEROL × 1 SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0.2M ammonium sulfate, 25% PEG 4000
Resolution 1.50 Å R-free 0.198
4PIJ X-ray crystal structure of the K11S/K63S double mutant of ubiquitin Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–75（75 aa）
Chain B 1–75（75 aa）
Mutation：K11S, K63S Mutation：K11S, K63S GOL GLYCEROL × 1 SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0.2M ammonium sulfate, 25% PEG 4000
Resolution 1.50 Å R-free 0.198
4PIJ X-ray crystal structure of the K11S/K63S double mutant of ubiquitin Deposited 2014-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–75（75 aa）
Chain B 1–75（75 aa）
Mutation：K11S, K63S Mutation：K11S, K63S GOL GLYCEROL × 1 SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0.2M ammonium sulfate, 25% PEG 4000
Resolution 1.50 Å R-free 0.198
4RF1 Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease in complex with ubiquitin (space group P63) Deposited 2014-09-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa） Fragment：UNP residues 1-75
Not recorded ZN ZINC ION × 1 PGO S-1,2-PROPANEDIOL × 5 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；20% PEG 4000, 0.1 M trisodium citrate, 20% isopropanol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.15 Å R-free 0.231
4S1Z Crystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin Deposited 2015-01-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；285 K；100mM MES, 200mM potassium iodide and 25% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 3.03 Å R-free 0.270
4S1Z Crystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin Deposited 2015-01-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；285 K；100mM MES, 200mM potassium iodide and 25% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 3.03 Å R-free 0.270
4S1Z Crystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin Deposited 2015-01-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；285 K；100mM MES, 200mM potassium iodide and 25% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 3.03 Å R-free 0.270
4S1Z Crystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin Deposited 2015-01-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；285 K；100mM MES, 200mM potassium iodide and 25% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 3.03 Å R-free 0.270
4S1Z Crystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin Deposited 2015-01-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–76（76 aa） Fragment：residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；285 K；100mM MES, 200mM potassium iodide and 25% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 3.03 Å R-free 0.270
4UG0 STRUCTURE OF THE HUMAN 80S RIBOSOME Deposited 2015-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 89-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 239 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
4V6X Structure of the human 80S ribosome Deposited 2013-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 84 PDB declaration: 89-meric
Chain Cm 77–128（52 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds using two pieces of filter paper, then plunge into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.00 Å
4XKL Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin Deposited 2015-01-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 ACT ACETATE ION × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3350
Resolution 2.10 Å R-free 0.243
4XKL Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin Deposited 2015-01-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 ACT ACETATE ION × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3350
Resolution 2.10 Å R-free 0.243
5AJ0 Cryo electron microscopy of actively translating human polysomes (POST state). Deposited 2015-02-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Am 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 326 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-KOH, PH 7.5, 100 MM KCL, 1.5 MM MGCL2, 0.5 MM SPERMIDINE, 0.04 MM SPERMINE, 1 MM DTT；pH 7.5；20 MM HEPES-KOH, PH 7.5, 100 MM KCL, 1.5 MM MGCL2, 0.5 MM SPERMIDINE, 0.04 MM SPERMINE, 1 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 93, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT FOR 2-4 SECONDS BEFORE PLUNGING,
Resolution 3.50 Å
5LKS Structure-function insights reveal the human ribosome as a cancer target for antibiotics Deposited 2016-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain Lm 1–128（128 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 224 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
5T2C CryoEM structure of the human ribosome at 3.6 Angstrom resolution Deposited 2016-08-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain g 1–128（128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6IP5 Cryo-EM structure of the CMV-stalled human 80S ribosome (Structure ii) Deposited 2018-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 2g 1–128（128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6IP6 Cryo-EM structure of the CMV-stalled human 80S ribosome with HCV IRES (Structure iii) Deposited 2018-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain 2g 1–128（128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6IP8 Cryo-EM structure of the HCV IRES dependently initiated CMV-stalled 80S ribosome (Structure iv) Deposited 2018-11-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 2g 1–128（128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6LQM Cryo-EM structure of a pre-60S ribosomal subunit - state C Deposited 2020-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain R 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 251 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
6OLE Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAs Deposited 2019-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain n 78–127（50 aa）
Not recorded MG MAGNESIUM ION × 31 ZN ZINC ION × 6 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6OLF Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA and PE tRNAs Deposited 2019-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain n 78–127（50 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 31 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6OLG Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA) Deposited 2019-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Am 78–127（50 aa）
Not recorded MG MAGNESIUM ION × 326 ZN ZINC ION × 5 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6OLI Structure of human ribosome nascent chain complex selectively stalled by a drug-like small molecule (USO1-RNC) Deposited 2019-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain n 78–127（50 aa）
Not recorded MG MAGNESIUM ION × 31 ZN ZINC ION × 6 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OLZ Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with PP tRNA Deposited 2019-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Am 78–127（50 aa）
Not recorded MG MAGNESIUM ION × 326 ZN ZINC ION × 5 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6OM0 Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with AP and PE tRNAs Deposited 2019-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain n 78–127（50 aa）
Not recorded MG MAGNESIUM ION × 31 ZN ZINC ION × 6 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6OM7 Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like small molecule with AA and PE tRNAs Deposited 2019-04-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain n 78–127（50 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 31 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6QZP High-resolution cryo-EM structure of the human 80S ribosome Deposited 2019-03-12 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 × 76 PDB declaration: 81-meric
Chain Lm 77–128（52 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 438 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 ZN ZINC ION × 8 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XA1 Structure of a drug-like compound stalled human translation termination complex Deposited 2020-06-03 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 × 77 PDB declaration: 83-meric
Chain Lm 77–128（52 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 190 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ZN ZINC ION × 8 K POTASSIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6Y0G Structure of human ribosome in classical-PRE state Deposited 2020-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 72 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6Y2L Structure of human ribosome in POST state Deposited 2020-02-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 80-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 193 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6Y57 Structure of human ribosome in hybrid-PRE state Deposited 2020-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 160 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6Y6X Tetracenomycin X bound to the human ribosome Deposited 2020-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 229 OCW Tetracenomycin X × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6Z6L Cryo-EM structure of human CCDC124 bound to 80S ribosomes Deposited 2020-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6Z6M Cryo-EM structure of human 80S ribosomes bound to EBP1, eEF2 and SERBP1 Deposited 2020-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6Z6N Cryo-EM structure of human EBP1-80S ribosomes (focus on EBP1) Deposited 2020-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6ZM7 SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex Deposited 2020-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6ZME SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex Deposited 2020-07-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 83 PDB declaration: 88-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 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
6ZMI SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complex Deposited 2020-07-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6ZMO SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complex Deposited 2020-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7AY1 Cryo-EM structure of USP1-UAF1 bound to mono-ubiquitinated FANCD2, and FANCI Deposited 2020-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain C 1–76（76 aa）
Mutation：GPGS expression tag ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7BHP Cryo-EM structure of the human Ebp1 - 80S ribosome Deposited 2021-01-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 45-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 41 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7F5S human delta-METTL18 60S ribosome Deposited 2021-06-22 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 × 42 PDB declaration: 45-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 279 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
7M3Q Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV) Deposited 2021-03-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–74（73 aa）
Not recorded SO4 SULFATE ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 6 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；1.5 M Ammonium Sulphate and 100 mM MES pH 6.0. Trypsin was added to the protein complex at a final concentration of 10 microgram per mL
Resolution 2.50 Å R-free 0.235
7OWC Structure of CYLD CAP-Gly3 (467-565) bound to Ub; orthorhobic space group Deposited 2021-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；291 K；35 % (w/v) PEG 1,000, 50 mM HEPES pH 7.3
Resolution 1.85 Å R-free 0.239
7UN3 Complex of UBE2O with NAP1L1 and ubiquitylated uL2 Deposited 2022-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7XNX High resolution cry-EM structure of the human 80S ribosome from SNORD127+/+ Kasumi-1 cells Deposited 2022-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 421 K POTASSIUM ION × 12 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7XNY High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cells Deposited 2022-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 421 K POTASSIUM ION × 12 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7ZF1 Structure of ubiquitinated FANCI in complex with FANCD2 and double-stranded DNA Deposited 2022-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
7ZH3 USP1 bound to ubiquitin conjugated to FANCD2 (focused refinement) Deposited 2022-04-05 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3.0 secs before plunging
Resolution 2.50 Å
7ZH4 USP1 bound to ML323 and ubiquitin conjugated to FANCD2 (focused refinement) Deposited 2022-04-05 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 1 JDA 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blotting for 3.0 seconds
Resolution 2.49 Å
8ADB Viral tegument-like DUBs Deposited 2022-07-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded CIT CITRIC ACID × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M BisTris propane pH 7.0, 2.0 M Ammonium citrate tribasic
Resolution 1.73 Å R-free 0.193
8CX9 Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an unusual allosteric mechanism Deposited 2022-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–77（77 aa）
Chain G 1–77（77 aa）
Not recorded ZN ZINC ION × 1 BR BROMIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；281 K；14.86 mg/ml SARS-CoV2C111S/UbV.CV2.1, 20% PEG 3350, 0.2 M sodium bromide, 0.1 M BIS-TRIS propane (pH 6.3), 50 mM lithium chloride. Cryoprotected in the same buffer plus 30% glycerol
Resolution 3.50 Å R-free 0.270
8CX9 Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an unusual allosteric mechanism Deposited 2022-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–77（77 aa）
Chain I 1–77（77 aa）
Not recorded ZN ZINC ION × 1 BR BROMIDE ION × 3 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；281 K；14.86 mg/ml SARS-CoV2C111S/UbV.CV2.1, 20% PEG 3350, 0.2 M sodium bromide, 0.1 M BIS-TRIS propane (pH 6.3), 50 mM lithium chloride. Cryoprotected in the same buffer plus 30% glycerol
Resolution 3.50 Å R-free 0.270
8CX9 Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an unusual allosteric mechanism Deposited 2022-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–77（77 aa）
Chain L 1–77（77 aa）
Not recorded ZN ZINC ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；281 K；14.86 mg/ml SARS-CoV2C111S/UbV.CV2.1, 20% PEG 3350, 0.2 M sodium bromide, 0.1 M BIS-TRIS propane (pH 6.3), 50 mM lithium chloride. Cryoprotected in the same buffer plus 30% glycerol
Resolution 3.50 Å R-free 0.270
8CX9 Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an unusual allosteric mechanism Deposited 2022-05-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–77（77 aa）
Chain J 1–77（77 aa）
Not recorded ZN ZINC ION × 1 BR BROMIDE ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；281 K；14.86 mg/ml SARS-CoV2C111S/UbV.CV2.1, 20% PEG 3350, 0.2 M sodium bromide, 0.1 M BIS-TRIS propane (pH 6.3), 50 mM lithium chloride. Cryoprotected in the same buffer plus 30% glycerol
Resolution 3.50 Å R-free 0.270
8IFD Dibekacin-added human 80S ribosome Deposited 2023-02-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain 2g 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 84D Dibekacin × 24 MG MAGNESIUM ION × 397 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.59 Å
8IFE Arbekacin-added human 80S ribosome Deposited 2023-02-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain 2g 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 84G Arbekacin × 23 MG MAGNESIUM ION × 410 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8IK6 pUbl depleted Parkin complex with pUbiquitin Deposited 2023-02-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane
Resolution 3.30 Å R-free 0.270
8IK6 pUbl depleted Parkin complex with pUbiquitin Deposited 2023-02-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane
Resolution 3.30 Å R-free 0.270
8IKM Trans complex of phospho parkin Deposited 2023-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.3 M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3 M Ammonium sulfate,1.0 M 8.5 Tris (base), BICINE, 25% v/v MPD; 25% PEG 1000, 25% w/v PEG 3350
Resolution 1.92 Å R-free 0.233
8IKT Ternary trans-complex of phospho-parkin with cis ACT and pUb Deposited 2023-03-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 GOL GLYCEROL × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.3 M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3 M Ammonium sulfate, Imidazole, MES monohydrate (acid), 25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350
Resolution 2.60 Å R-free 0.236
8IKV pUbl depleted phospho-Parkin(K211N,R163D) in complex with pUb Deposited 2023-03-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
Resolution 2.35 Å R-free 0.217
8IKV pUbl depleted phospho-Parkin(K211N,R163D) in complex with pUb Deposited 2023-03-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
Resolution 2.35 Å R-free 0.217
8IPJ Crystal structure of the Legionella effector protein MavL with ADPR-Ub Deposited 2023-03-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–72（72 aa）
Not recorded AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions COUNTER-DIFFUSION；289.15 K；0.1 M HEPES/sodium hydroxide pH7.5, 20% polyethylene glycol 10000
Resolution 2.00 Å R-free 0.222
8JDJ Structure of the Human cytoplasmic Ribosome with human tRNA Asp(Q34) and mRNA(GAU) Deposited 2023-05-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 80-meric
Chain r 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 539 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；The Buffer pH was adjusted to 7.4 using KOH.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8JDK Structure of the Human cytoplasmic Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU) Deposited 2023-05-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 80-meric
Chain r 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 539 MAN alpha-D-mannopyranose × 2 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；The Buffer pH was adjusted to 7.4 using KOH.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.26 Å
8JDL Structure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (non-rotated state) Deposited 2023-05-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 79-meric
Chain r 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 539 GAL beta-D-galactopyranose × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；The Buffer pH was adjusted to 7.4 using KOH.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.42 Å
8JDM Structure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (rotated state) Deposited 2023-05-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 80-meric
Chain r 1–128（128 aa）
Not recorded GAL beta-D-galactopyranose × 2 MG MAGNESIUM ION × 520 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；The Buffer pH was adjusted to 7.4 using KOH.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.67 Å
8K2C Cryo-EM structure of the human 80S ribosome with Tigecycline Deposited 2023-07-12 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 × 81 PDB declaration: 86-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 259 T1C TIGECYCLINE × 9 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8OHD 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native) Deposited 2023-03-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 220 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8OJ0 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native) Deposited 2023-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 220 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OJ5 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution) Deposited 2023-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 220 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8OJ8 60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native) Deposited 2023-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 220 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8QFD UFL1 E3 ligase bound 60S ribosome Deposited 2023-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain m 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 161 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM HEPES pH 7.5, 50 mM KCl, 5 mM MgCl2, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8QOI Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical modifications and ions in RNA Deposited 2023-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 292 K POTASSIUM ION × 108 SPD SPERMIDINE × 2 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；Titan Krios sample is prepared with Sodium cacodylate buffer. CryoARM 300 sample is prepared with Hepes buffer.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8QYX Human 60S ribosomal subunit Deposited 2023-10-26 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 × 41 PDB declaration: 44-meric
Chain g1 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 186 PUT 1,4-DIAMINOBUTANE × 7 K POTASSIUM ION × 46 ZN ZINC ION × 5 SPD SPERMIDINE × 7 SPM SPERMINE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.78 Å
8UKB In situ HHT and CHX treated human hibernating state without E-tRNA 80S ribosome Deposited 2023-10-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 255 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 WV3 4-{(2R)-2-[(1R,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8XSX Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2 Deposited 2024-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 259 T1C TIGECYCLINE × 7 ZN ZINC ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8XSY Cryo-EM structure of the human 80S ribosome with Tigecycline, e-tRNA and CCDC124 (40S head Swivelled) Deposited 2024-01-10 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 × 81 PDB declaration: 86-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 255 T1C TIGECYCLINE × 8 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8XSZ Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA and P-tRNA Deposited 2024-01-10 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 × 79 PDB declaration: 86-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 248 T1C TIGECYCLINE × 5 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Y0W dormant ribosome with eIF5A, eEF2 and SERBP1 Deposited 2024-01-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 226 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50mM HEPES, pH7.5, 100mM KOAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8Y0X Dormant ribosome with SERBP1 Deposited 2024-01-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50mM HEPES, pH7.4, 100mM KoAc, 5mM Mg(OAc)2, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8YOO Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline Deposited 2024-03-13 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 × 77 PDB declaration: 81-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 257 T1C TIGECYCLINE × 6 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8YOP Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline Deposited 2024-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9B0P In situ human Hibernating class1 80S ribosome Deposited 2024-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.82 Å
9B0Q In situ human top-back di-ribosome structure (Composite map) Deposited 2024-03-12 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 × 160 PDB declaration: 172-meric
Chain Lm 77–128（52 aa）
Chain lm 77–128（52 aa）
Not recorded ZN ZINC ION × 12 MG MAGNESIUM ION × 510 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9B0S In situ human top-top di-ribosome structure (Composite map) Deposited 2024-03-12 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 × 158 PDB declaration: 171-meric
Chain Lm 77–128（52 aa）
Chain lm 77–128（52 aa）
Not recorded ZN ZINC ION × 12 MG MAGNESIUM ION × 510 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9C3H Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site. Deposited 2024-06-01 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 × 77 PDB declaration: 83-meric
Chain Lo 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 326 K POTASSIUM ION × 94 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
9FQZ CRYO-EM STRUCTURE OF HCT15 POLYSOMES BOUND TO EEF2, EBP1, AND SERBP1 Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain Lm 1–128（128 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 271 K POTASSIUM ION × 104 ZN ZINC ION × 8 PUT 1,4-DIAMINOBUTANE × 7 HYG HYGROMYCIN B × 1 SPD SPERMIDINE × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ANM ANISOMYCIN × 1 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 232 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
9GMO eIF6-bound pre-60S large ribosomal subunit incorporating mutant uL16 Deposited 2024-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric
Chain g 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 227 K POTASSIUM ION × 155 NA SODIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.59 Å
9GUL Structure of FLuc-XBP1u+ stalled human 60S ribosome nascent chain complex Deposited 2024-09-19 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 × 42 PDB declaration: 46-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 284 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9GY4 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map) Deposited 2024-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 219 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9I14 CRYO-EM STRUCTURE OF HCT15 POLYSOMES IN HYBRID-PRE STATE Deposited 2025-01-15 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: 82-meric
Chain Lm 1–128（128 aa）
Not recorded K POTASSIUM ION × 40 MG MAGNESIUM ION × 267 NA SODIUM ION × 23 SPD SPERMIDINE × 1 PUT 1,4-DIAMINOBUTANE × 1 ZN ZINC ION × 7 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9I2D NMT1-NAC bound human RNC with 10 amino acid ARF1-linker Deposited 2025-01-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.19 Å
9I2E NMT1-NAC bound human ribosome (combined translational states) Deposited 2025-01-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9KZU Cryo-EM structure of the HCV IRES-dependently initiated CMV-stalled 80S ribosome (non-rotated state) in complexed with eIF3 Deposited 2024-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 85 PDB declaration: 92-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 81 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9KZX Cryo-EM structure of the HCV IRES-dependently initiated CMV-stalled 80S ribosome (rotated state) in complexed with eIF3 Deposited 2024-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 85 PDB declaration: 93-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 66 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9M0P Cryo-EM structure of human 80S ribosome in complex with montanine Deposited 2025-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 78-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 6 A1L8F (1S,13S,15S,16S)-16-methoxy-5,7-dioxa-12-azapentacyclo[10.6.1.02,10.04,8.013,18]nonadeca-2,4(8),9,17-tetraen-15-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9N9J Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon Deposited 2025-02-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 70-meric
Chain Lm 1–128（128 aa）
Not recorded ELU phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate × 1 MG MAGNESIUM ION × 226 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；HEPES buffer was adjusted to pH 7.4 with potassium hydroxide.
cryo-EM vitrification conditions Cryogen ETHANE；Three microliters of affinity-purified RTCs were applied to the grid, incubated for 60 seconds, blotted for 7 seconds, drained for 0.5 seconds, and frozen in liquid nitrogen-cooled ethane.
Resolution 3.20 Å
9O3V Human 80S ribosome stalled on MYC nascent chain Deposited 2025-04-07 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 × 76 PDB declaration: 82-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 352 K POTASSIUM ION × 165 SPD SPERMIDINE × 14 PUT 1,4-DIAMINOBUTANE × 7 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Tris, 100mM KOAc, 7.5mM MgOAc, 0.25mM Spermidine, 2mM DTT, 0.05% w/v b-OG
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9O3W Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain Deposited 2025-04-07 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 × 76 PDB declaration: 82-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 170 PUT 1,4-DIAMINOBUTANE × 7 SPD SPERMIDINE × 14 A1B75 (2R,3S,4S)-4-hydroxy-2-[(4-methoxyphenyl)methyl]pyrrolidin-3-yl {2-[(2S)-pyrrolidin-2-yl]ethyl}carbamate × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 MG MAGNESIUM ION × 371 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Tris, 100mM KOAc, 7.5mM MgOAc, 0.25mM Spermidine, 2mM DTT, 0.05% w/v b-OG, 50uM IDB-001
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
9O3Y Human 80S ribosome bound to IDB-002 stalled on FPAK-containing nascent chain Deposited 2025-04-07 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 × 76 PDB declaration: 82-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 168 SPD SPERMIDINE × 14 PUT 1,4-DIAMINOBUTANE × 7 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 MG MAGNESIUM ION × 332 A1B76 (2R,3S,4S)-4-hydroxy-2-[(4-methoxyphenyl)methyl]pyrrolidin-3-yl [(3-fluorophenyl)methyl]carbamate × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Tris, 100mM KOAc, 7.5mM MgOAc, 0.25mM Spermidine, 2mM DTT, 0.05% w/v b-OG, 50uM IDB-001
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9P6Z In situ human P-Z state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
9P72 In situ human P-E state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9P73 In situ human eEF2-A/P-P/E state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 218 ZN ZINC ION × 6 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
9P76 In situ human eEF1A-A/T-P state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9P78 In situ human Hibernating rotate 3 with E-site tRNA state 80S ribosome Deposited 2025-06-20 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 Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9P79 In situ human Hibernating rotate3 with Z site tRNA state 80S ribosome Deposited 2025-06-20 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 Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9P7A In situ human hibernating class2 80S ribosome Deposited 2025-06-20 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 Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
9P7C In situ human Hibernating class3 80S ribosome Deposited 2025-06-20 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 Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9P7D In situ human Hibernating class4 80S ribosome Deposited 2025-06-20 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 Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
9P7E In situ human Hibernating class5 80S ribosome Deposited 2025-06-20 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 Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.59 Å
9P7F In situ HHT and CHX treated A-P state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Lm 77–128（52 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9P7G In situ HHT and CHX treated A-P-Z state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 85-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 ZN ZINC ION × 6 SPM SPERMINE × 7 SPD SPERMIDINE × 10 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
9P7H In situ HHT and CHX treated human eEF1A-A/T-P state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.68 Å
9P7I In situ HHT and CHX treated human eEF1A-A/T-P-Z state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.69 Å
9P7J In situ HHT and CHX treated human P state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
9P7K In situ human post eEF1A-A/T-P-E state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9P7L In situ human Post-eEF1A-AT-P state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
9P7N In situ human Post-eEF1A-A/T-P-Z state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9P7O In situ human AT-P-Z state ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
9P7W In situ human A-P state 80S ribosome Deposited 2025-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 ZN ZINC ION × 6 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
9P7X In situ human A-P-Z state 80S ribosome Deposited 2025-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 85-meric
Chain Lm 77–128（52 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9P7Y In situ human A-P-E state 80S ribosome Deposited 2025-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 85-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 ZN ZINC ION × 6 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
9P8B In situ human eEF1A-A/T-P-E state 80S ribosome Deposited 2025-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
9P8C In situ human Hibernating class1 (rotate3) without E tRNA state 80S ribosome Deposited 2025-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 85-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
9P8H In situ human A/P-P/E state 80S ribosome Deposited 2025-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 218 ZN ZINC ION × 6 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9P8I In situ HHT and CHX treated human P-Z state 80S ribosome Deposited 2025-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.89 Å
9P9H In situ human unrotated hibernating with CCDC124 state 80S ribosome Deposited 2025-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.84 Å
9P9I In situ human unrotated hibernating without CCDC124 state 80S ribosome Deposited 2025-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.77 Å
9P9J In situ human 60S ribosome Deposited 2025-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 191 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
9P9K In situ human 60S ribosome with EIF6 Deposited 2025-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 191 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9PA7 In situ human 80S consensus ribosome with EBP1 Deposited 2025-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 225 SPM SPERMINE × 8 SPD SPERMIDINE × 12 K POTASSIUM ION × 75 ZN ZINC ION × 7 PUT 1,4-DIAMINOBUTANE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.67 Å
9PBE In situ human 80S ribosome (composite map) Deposited 2025-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 225 SPM SPERMINE × 8 SPD SPERMIDINE × 12 K POTASSIUM ION × 75 ZN ZINC ION × 7 PUT 1,4-DIAMINOBUTANE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.19 Å
9PKG In situ human P state 80S ribosome Deposited 2025-07-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain Lm 77–128（52 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
9PL1 Structure of metastable folding intermediate of V17A/V26A ubiquitin derived from pressure-jump NMR data Deposited 2025-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：V17A, V26A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 25；Pressure 1
NMR sample composition 200 uM [U-100% 13C; U-100% 15N; U-80% 2H] Ubq V17A/V26A, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 200 uM [U-100% 15N] Ubq V17A/V26A, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
9QLO NMT1-NAC bound human RNC with full length ARF1 - State 1 Deposited 2025-03-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 191 G3D GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
9QLP NMT1-NAC bound human RNC with full length ARF1 - State 2 Deposited 2025-03-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 191 G3D GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
9QLQ NMT1-NAC bound human RNC with full length ARF1 - alternative State Deposited 2025-03-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
9RPV Structure of the ZAK-bound human disome Deposited 2025-06-25 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: 168-meric
Chain Lm 1–128（128 aa）
Chain Mm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 830 ZN ZINC ION × 7 ANM ANISOMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.35 Å
9RU7 WT-HEK 80S ribosome bound to Kozak mRNA (WT-Kozak) Deposited 2025-07-03 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 × 75 PDB declaration: 82-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 17 MG MAGNESIUM ION × 74 C CYTIDINE-5'-MONOPHOSPHATE × 2 NA SODIUM ION × 7 ZN ZINC ION × 5 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9RU8 WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU) Deposited 2025-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 80-meric
Chain Lm 1–128（128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9RU9 RPS26dC HEK mutant 80S ribosome bound to Kozak mRNA (RPS26dC-Kozak) Deposited 2025-07-03 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 × 75 PDB declaration: 82-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.97 Å
9RUA RPS26dC HEK mutant 80S ribosome bound to TISU mRNA (RPS26dC-TISU) Deposited 2025-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 80-meric
Chain Lm 1–128（128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.90 Å
9RUC WT-HEK 80S ribosome bound to H2B mRNA (WT-H2B) Deposited 2025-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 80-meric
Chain Lm 1–127（127 aa）
Not recorded MG MAGNESIUM ION × 223 K POTASSIUM ION × 51 NA SODIUM ION × 8 ZN ZINC ION × 6 HYG HYGROMYCIN B × 1 SPD SPERMIDINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9S3B NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 1 Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9S3C NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2 Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.42 Å
9S3D NAC bound human RNC with 58 amino acid ARF1-linker Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain Lm 1–128（128 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.32 Å
9SPF CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE Deposited 2025-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 83-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 151 MG MAGNESIUM ION × 225 NA SODIUM ION × 35 SPD SPERMIDINE × 19 PUT 1,4-DIAMINOBUTANE × 9 ZN ZINC ION × 7 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9SPI CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINE Deposited 2025-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 83-meric
Chain Lm 1–128（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PUT 1,4-DIAMINOBUTANE × 8 SPD SPERMIDINE × 18 MG MAGNESIUM ION × 195 K POTASSIUM ION × 75 ZN ZINC ION × 7 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å

153 other PDB entries and 174 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL40_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–75； UniProt 1–75

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

SAXS scattering curve SAXS Profile

SAXS profile for 4rf0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4rf0
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id4rf0
Deposition date deposition_date2014-09-24
Structure title titleCrystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease in complex with ubiquitin (space group P6522)
Keywords keywordszinc ribbon, deubiquitinase, papain-like protease, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier24.02 Å
Radius of gyration Rg (electron density) rg_electron23.15 Å
Forward intensity I(0) i034086300.00
Molecular weight molecular_weight43979.0 kDa
Excluded volume excluded_volume54631 ų
Envelope volume envelope_volume65631 ų
Hydration-shell volume shell_volume24391 ų
Envelope diameter envelope_diameter83.3 Å
Shell Rg shell_rg29.34 Å
Envelope Rg envelope_rg23.49 Å
Shape Rg shape_rg23.15 Å
Total Rg total_rg23.89 Å
Total atoms total_atoms3070
Residues n_residues393
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax82.8 Å
Rg (real space) rg_real24.04 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real3.4090e+07
I(0) uncertainty (real space) i0_real_error4.9820e+05
Rg (reciprocal space) rg_reciprocal24.04 Å
I(0) (reciprocal space) i0_reciprocal34090000.0000
Solution quality estimate total_estimate0.6617
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.5 Å
Skewness Skewness skewness0.415
Kurtosis Kurtosis kurtosis-0.157
Angular range angular_range— – 0.3300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6878000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.795; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 0.947; Smooth: 0.965
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd4rf0a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd4rf0a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.23 — Papain-like viral protease catalytic domain
Domain ID domain_idd4rf0b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related

CATH v4.4 (3 domains)

Domain ID domain_id4rf0A01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily540 — Papain-like viral protease, N-terminal domain
Domain ID domain_id4rf0A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily1190 — Papain-like viral protease, thumb domain
Domain ID domain_id4rf0A03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily1680 —
▶

8. Citations (1)

▶

9. Files and Curves (10)