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6f4q

Human JMJD5 (Q275C) in complex with Mn(II), NOG and RPS6-A138C (129-144) (complex-2)

Method: X-RAY DIFFRACTION Dmax: 59.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

JmjC domain-containing protein 5

Homo sapiens

UniProt Q8N371

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 221–454 Mutation：C217A, C232A, Q275C, C295A, C384A MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1M Bis-Tris pH 6.0, 19.3 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio) Resolution 1.12 Å R-free 0.153

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 6F4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3UYJ Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG Deposited 2011-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 173–416（244 aa） Fragment：Catalytic core domain, UNP residues 173-416
Chain B 173–416（244 aa） Fragment：Catalytic core domain, UNP residues 173-416
Not recorded NI NICKEL (II) ION × 2 AKG 2-OXOGLUTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；291 K；8% PEG3350, 0.1M HepesNa pH 7.5, EVAPORATION, temperature 291K
Resolution 2.35 Å R-free 0.253
4AAP Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (NOG) Deposited 2011-12-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–454（237 aa） Fragment：JMJD5 DOMAIN, RESIDUES 218-454
Not recorded ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 16% PEG_3350, 0.007M NICL, 0M CDCL, 0.007M MGCL, 0.1M HEPES PH 7.3
Resolution 2.60 Å R-free 0.253
4AAP Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (NOG) Deposited 2011-12-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 218–454（237 aa） Fragment：JMJD5 DOMAIN, RESIDUES 218-454
Not recorded ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 16% PEG_3350, 0.007M NICL, 0M CDCL, 0.007M MGCL, 0.1M HEPES PH 7.3
Resolution 2.60 Å R-free 0.253
4GAZ Crystal Structure of a Jumonji Domain-containing Protein JMJD5 Deposited 2012-07-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 176–416（241 aa） Fragment：JmjC domain, UNP residues 176-416
Not recorded NI NICKEL (II) ION × 1 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；289 K；100mM HEPES, 9% PEG 3350 (w/v), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.81 Å R-free 0.274
4GAZ Crystal Structure of a Jumonji Domain-containing Protein JMJD5 Deposited 2012-07-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 176–416（241 aa） Fragment：JmjC domain, UNP residues 176-416
Not recorded NI NICKEL (II) ION × 1 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；289 K；100mM HEPES, 9% PEG 3350 (w/v), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.81 Å R-free 0.274
4GJY JMJD5 in complex with N-Oxalylglycine Deposited 2012-08-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa） Fragment：JmjC Domain (UNP Residues 183-416)
Non-standard monomer：Yes (specific site not provided by mmCIF) CO COBALT (II) ION × 1 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；4.5% PEG 3000, 0.1 M Bis-Tris pH 5.5, 0.05 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.25 Å R-free 0.161
4GJZ JMJD5 in complex with 2-oxoglutarate Deposited 2012-08-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa） Fragment：JmjC Domain (UNP Residues 183-416)
Not recorded CO COBALT (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 BME BETA-MERCAPTOETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；9.5% PEG 3000, 0.1 M Bis-Tris pH 6.2, 0.05 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.05 Å R-free 0.163
4QU1 Crystal structure of human JMJD5 jmj-c domain Deposited 2014-07-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa） Fragment：jmj-c domain (UNP residues 183-416)
Not recorded NI NICKEL (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, pH 7.0, 8% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.57 Å R-free 0.174
5FBJ Complex structure of JMJD5 and substrate Deposited 2015-12-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa）
Not recorded AKG 2-OXOGLUTARIC ACID × 1 NMM (2S)-2-amino-5-[(N-methylcarbamimidoyl)amino]pentanoic acid × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；281 K；PEG3350 HEPEPS-Na
Resolution 2.42 Å R-free 0.246
6AVS Complex structure of JMJD5 and Symmetric Monomethyl-Arginine (MMA) Deposited 2017-09-04 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 221–454（234 aa）
Not recorded ZN ZINC ION × 1 NMM (2S)-2-amino-5-[(N-methylcarbamimidoyl)amino]pentanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M HEPES pH 7.0 8% PEG 3350
Resolution 2.02 Å R-free 0.272
6AX3 Complex structure of JMJD5 and Symmetric Dimethyl-Arginine (SDMA) Deposited 2017-09-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 222–454（233 aa）
Not recorded 2MR N3, N4-DIMETHYLARGININE × 1 AKG 2-OXOGLUTARIC ACID × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M HEPES pH 7.0 8% PEG 3350
Resolution 2.25 Å R-free 0.259
6F4M Human JMJD5 in its apo form. Deposited 2017-11-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 182–416（235 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M Bis-Tris pH 6.5, 22.5 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio)
Resolution 1.71 Å R-free 0.186
6F4N Human JMJD5 in complex with MN and 2OG. Deposited 2017-11-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 153–416（264 aa）
Not recorded MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1 M Bis-Tris pH 6.0, 21.4 % PEG3350, 0.07 M MgCl2, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)
Resolution 2.54 Å R-free 0.230
6F4N Human JMJD5 in complex with MN and 2OG. Deposited 2017-11-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 153–416（264 aa）
Not recorded MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1 M Bis-Tris pH 6.0, 21.4 % PEG3350, 0.07 M MgCl2, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)
Resolution 2.54 Å R-free 0.230
6F4O Human JMJD5 in complex with Mn(II) and Succinate. Deposited 2017-11-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa）
Not recorded MN MANGANESE (II) ION × 1 SIN SUCCINIC ACID × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 2:1 ratio)
Resolution 1.28 Å R-free 0.174
6F4P Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1) Deposited 2017-11-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 183–416（234 aa） Fragment：Catalytic domain, UNP residues 183-416
Not recorded MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1M Bis-Tris pH 6.0, 26.4 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)
Resolution 1.45 Å R-free 0.168
6F4R Human JMJD5 (N308C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-3) Deposited 2017-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa）
Mutation：C217A, C232A, C295A, N308C, C384A Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；298 K；0.1M Bis-Tris pH 5.8, 25 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio)
Resolution 1.30 Å R-free 0.162
6F4S Human JMJD5 (N308C) in complex with Mn(II), 2OG and RCCD1 (139-143) (complex-4) Deposited 2017-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 183–416（234 aa）
Mutation：C217A, C232A, N308C MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1M Bis-Tris pH 6.5, 29 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)
Resolution 1.46 Å R-free 0.152
6F4T Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5) Deposited 2017-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa） Fragment：Catalytic domain, UNP residues 183-416
Mutation：C217A, C232A, W414C Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1M Bis-Tris pH 6.5, 17.1 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio)
Resolution 1.22 Å R-free 0.154
6I9L JmjC domain-containing protein 5 (JMJD5) in complex with Mn and pyridine-2,4-dicarboxylic acid (2,4-PDCA) Deposited 2018-11-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa）
Not recorded MN MANGANESE (II) ION × 1 PD2 PYRIDINE-2,4-DICARBOXYLIC ACID × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M BIS-TRIS PH 6.5, 15.0 % PEG3350, 0.002 M MNCL2, 300 NL SITTING DROPS (SAMPLE:WELL, 2:1 RATIO)
Resolution 1.53 Å R-free 0.164
6I9M JmjC domain-containing protein 5 (JMJD5) in complex with Mn and R-2-hydroxyglutarate Deposited 2018-11-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa）
Not recorded MN MANGANESE (II) ION × 1 2HG (2R)-2-hydroxypentanedioic acid × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2
Resolution 1.65 Å R-free 0.181
6I9N JmjC domain-containing protein 5 (JMJD5) in complex with Mn and L-2-hydroxyglutarate Deposited 2018-11-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa）
Not recorded MN MANGANESE (II) ION × 1 S2G (2S)-2-HYDROXYPENTANEDIOIC ACID × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2
Resolution 1.36 Å R-free 0.159
7DYT Human JMJD5 in complex with MN and 5-((4-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid. Deposited 2021-01-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa）
Not recorded MN MANGANESE (II) ION × 1 HR3 5-((4-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride
Resolution 1.62 Å R-free 0.189
7DYU Human JMJD5 in complex with MN and 5-((4-phenylbutyl)amino)pyridine-2,4-dicarboxylic acid. Deposited 2021-01-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa）
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 MN MANGANESE (II) ION × 1 HR9 5-(4-phenylbutylamino)pyridine-2,4-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride
Resolution 1.72 Å R-free 0.195
7DYV Human JMJD5 in complex with MN and 5-(benzylamino)pyridine-2,4-dicarboxylic acid. Deposited 2021-01-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa）
Not recorded MN MANGANESE (II) ION × 1 HRF 5-(benzylamino)pyridine-2,4-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride
Resolution 1.92 Å R-free 0.240
7DYW Human JMJD5 in complex with MN and 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid. Deposited 2021-01-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa）
Not recorded HRL 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride
Resolution 2.13 Å R-free 0.239
7DYX Human JMJD5 in complex with MN and 5-((2-cyclopropylbenzyl)amino)pyridine-2,4-dicarboxylic acid. Deposited 2021-01-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa）
Not recorded MN MANGANESE (II) ION × 1 HRR 5-((2-cyclopropylbenzyl)amino)pyridine-2,4-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride
Resolution 2.27 Å R-free 0.280
7UQ3 JmjC domain-containing protein 5 (JMJD5) in complex with Mn and (S)-2-(1-hydroxy-2,5-dioxopyrrolidin-3-yl)acetic acid Deposited 2022-04-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–416（234 aa）
Not recorded MN MANGANESE (II) ION × 1 O2U [(3S)-1-hydroxy-2,5-dioxopyrrolidin-3-yl]acetic acid × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；Sample: 22 mg/mL JMJD5, 1.5 mM MnCl2, 5 mM compound (IS-52); Reservoir: 0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2; Cryo-protection: 25% (v/v) glycerol; Method: 300 nL sitting drops (sample:well, 2:1 ratio)
Resolution 1.49 Å R-free 0.135

25 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KDM8_HUMAN
Isoform Q8N371-3
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 22–255； UniProt 221–454

40S ribosomal protein S6

OrganismNot specified

UniProt P62753

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 129–144 Mutation：A138C No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1M Bis-Tris pH 6.0, 19.3 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio) Resolution 1.12 Å R-free 0.153

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 6F4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
22TU Human 80S ribosome in complex with DHX29 Deposited 2026-01-22 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 × 77 PDB declaration: 83-meric
Chain SG 1–249（249 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain AG 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.70 Å
28ZU human 48S PIC with Kozak mRNA and eIF1A W70A mutant Deposited 2026-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 41-meric
Chain SG 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
28ZV human 48S PIC with mRNA (non-Kozak) Deposited 2026-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 41-meric
Chain SG 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.90 Å
28ZX human 48S PIC with mRNA (Kozak_1) Deposited 2026-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain SG 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.80 Å
28ZY human 48S PIC with mRNA (Kozak_2) Deposited 2026-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain SG 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
4UG0 STRUCTURE OF THE HUMAN 80S RIBOSOME Deposited 2015-03-20 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: 89-meric
Chain SG 1–249（249 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 84 PDB declaration: 89-meric
Chain AG 1–249（249 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
5A2Q Structure of the HCV IRES bound to the human ribosome Deposited 2015-05-21 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 × 36 PDB declaration: 38-meric
Chain G 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 98 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer 20MM HEPES, 100 MM KCL, 5 MM MGCL2；pH 7.6；20MM HEPES, 100 MM KCL, 5 MM MGCL2
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；FROZEN ON 200 MESH QUANTIFOIL R 2 2 HOLEY CARBON GRIDS WITH A THIN CONTINUOUS CARBON SUPPORT FILM APPLIED IN ETHANE PROPANE MIX
Resolution 3.90 Å
5AJ0 Cryo electron microscopy of actively translating human polysomes (POST state). Deposited 2015-02-19 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 × 79 PDB declaration: 86-meric
Chain BG 1–249（249 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
5FLX Mammalian 40S HCV-IRES complex Deposited 2015-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 35-meric
Chain G 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 74 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer 20MM TRIS-HCL, 7.5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT；pH 7.6；20MM TRIS-HCL, 7.5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 93, INSTRUMENT- FEI VITROBOT MARK I, METHOD- BLOT FOR 2-4 SECONDS BEFORE PLUNGING,
Resolution 3.90 Å
5LKS Structure-function insights reveal the human ribosome as a cancer target for antibiotics Deposited 2016-07-23 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 SG 1–249（249 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
5OA3 Human 40S-eIF2D-re-initiation complex Deposited 2017-06-20 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 × 35 PDB declaration: 38-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.20 Å R-free 0.325
5T2C CryoEM structure of the human ribosome at 3.6 Angstrom resolution Deposited 2016-08-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AK 1–249（249 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
5VYC Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1. Deposited 2017-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain G1 1–249（249 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298.15 K；50 mM HEPES-NaOH, 50 mM NH4 acetate, 50 mM NH4Cl, 1 mM Mg acetate, 2 mM CaCl2, 3% PEG 20000, 3% PEG 3350, 2 mM TCEP, pH 8.1
Resolution 6.00 Å R-free 0.321
5VYC Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1. Deposited 2017-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain G2 1–249（249 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298.15 K；50 mM HEPES-NaOH, 50 mM NH4 acetate, 50 mM NH4Cl, 1 mM Mg acetate, 2 mM CaCl2, 3% PEG 20000, 3% PEG 3350, 2 mM TCEP, pH 8.1
Resolution 6.00 Å R-free 0.321
5VYC Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1. Deposited 2017-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain G3 1–249（249 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298.15 K；50 mM HEPES-NaOH, 50 mM NH4 acetate, 50 mM NH4Cl, 1 mM Mg acetate, 2 mM CaCl2, 3% PEG 20000, 3% PEG 3350, 2 mM TCEP, pH 8.1
Resolution 6.00 Å R-free 0.321
5VYC Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1. Deposited 2017-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain G4 1–249（249 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298.15 K；50 mM HEPES-NaOH, 50 mM NH4 acetate, 50 mM NH4Cl, 1 mM Mg acetate, 2 mM CaCl2, 3% PEG 20000, 3% PEG 3350, 2 mM TCEP, pH 8.1
Resolution 6.00 Å R-free 0.321
5VYC Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1. Deposited 2017-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain G5 1–249（249 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298.15 K；50 mM HEPES-NaOH, 50 mM NH4 acetate, 50 mM NH4Cl, 1 mM Mg acetate, 2 mM CaCl2, 3% PEG 20000, 3% PEG 3350, 2 mM TCEP, pH 8.1
Resolution 6.00 Å R-free 0.321
5VYC Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1. Deposited 2017-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain G6 1–249（249 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；298.15 K；50 mM HEPES-NaOH, 50 mM NH4 acetate, 50 mM NH4Cl, 1 mM Mg acetate, 2 mM CaCl2, 3% PEG 20000, 3% PEG 3350, 2 mM TCEP, pH 8.1
Resolution 6.00 Å R-free 0.321
6F4P Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1) Deposited 2017-11-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 129–144（16 aa） Fragment：UNP residues 129-144
Not recorded MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1M Bis-Tris pH 6.0, 26.4 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)
Resolution 1.45 Å R-free 0.168
6FEC Human cap-dependent 48S pre-initiation complex Deposited 2017-12-31 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain q 1–237（237 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Tris HCl, 50 mM KOAc, 2.5 mM MgCl2, 2 mM DTT, 0.25 mM spermidine 0.25 mM GMPPNP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
6G18 Cryo-EM structure of a late human pre-40S ribosomal subunit - State C Deposited 2018-03-20 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 × 34 PDB declaration: 35-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6G4S Cryo-EM structure of a late human pre-40S ribosomal subunit - State B Deposited 2018-03-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 33-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6G4W Cryo-EM structure of a late human pre-40S ribosomal subunit - State A Deposited 2018-03-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 31-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6G51 Cryo-EM structure of a late human pre-40S ribosomal subunit - State D Deposited 2018-03-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 38-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6G53 Cryo-EM structure of a late human pre-40S ribosomal subunit - State E Deposited 2018-03-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6G5H Cryo-EM structure of a late human pre-40S ribosomal subunit - Mature Deposited 2018-03-29 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 × 34 PDB declaration: 35-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6G5I Cryo-EM structure of a late human pre-40S ribosomal subunit - State R Deposited 2018-03-29 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 × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6IP5 Cryo-EM structure of the CMV-stalled human 80S ribosome (Structure ii) Deposited 2018-11-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 3H 1–249（249 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain 3H 1–249（249 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 3H 1–249（249 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
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 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: 83-meric
Chain SG 1–237（237 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 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: 83-meric
Chain SG 1–237（237 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 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: 85-meric
Chain BG 1–232（232 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 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: 83-meric
Chain SG 1–237（237 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 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 BG 1–232（232 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 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: 83-meric
Chain SG 1–237（237 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 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: 83-meric
Chain SG 1–237（237 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 SG 1–237（237 aa）
Not recorded 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 SG 1–228（228 aa）
Not recorded 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 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: 83-meric
Chain SG 1–249（249 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 mutation/modification 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 SG 1–249（249 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 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 SG 1–249（249 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
6YBW Structure of a human 48S translational initiation complex - 40S body Deposited 2020-03-18 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 × 24 PDB declaration: 26-meric
Chain S 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 60 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6Z6L Cryo-EM structure of human CCDC124 bound to 80S ribosomes Deposited 2020-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain SG 1–249（249 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 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: 84-meric
Chain SG 1–249（249 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 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: 84-meric
Chain SG 1–249（249 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
6ZLW SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit Deposited 2020-07-01 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 × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6ZM7 SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex Deposited 2020-07-01 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 × 81 PDB declaration: 86-meric
Chain SG 1–249（249 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 mutation/modification 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 SG 1–249（249 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 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 SG 1–249（249 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 mutation/modification 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 SG 1–249（249 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
6ZMT SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex Deposited 2020-07-03 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 × 34 PDB declaration: 35-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6ZMW Structure of a human 48S translational initiation complex Deposited 2020-07-04 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 × 54 PDB declaration: 57-meric
Chain S 1–249（249 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 89 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ZN5 SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex - state 2 Deposited 2020-07-06 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 × 35 PDB declaration: 36-meric
Chain G 1–230（230 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6ZOJ SARS-CoV-2-Nsp1-40S complex, composite map Deposited 2020-07-07 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 × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 166 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.80 Å
6ZOK SARS-CoV-2-Nsp1-40S complex, focused on body Deposited 2020-07-07 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 × 21 PDB declaration: 22-meric
Chain G 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 109 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.80 Å
6ZON SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1 Deposited 2020-07-07 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 × 47 PDB declaration: 48-meric
Chain r 1–249（249 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6ZP4 SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2 Deposited 2020-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain r 1–249（249 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6ZUO Human RIO1(kd)-StHA late pre-40S particle, structural state A (pre 18S rRNA cleavage) Deposited 2020-07-23 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 × 34 PDB declaration: 35-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6ZV6 Human RIO1(kd)-StHA late pre-40S particle, structural state B (post 18S rRNA cleavage) Deposited 2020-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 35-meric
Chain G 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 3 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6ZVH EDF1-ribosome complex Deposited 2020-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 37-meric
Chain G 1–237（237 aa）
Not recorded MG MAGNESIUM ION × 30 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6ZVJ Structure of a human ABCE1-bound 43S pre-initiation complex - State II Deposited 2020-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 51-meric
Chain r 2–223（222 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6ZXD Cryo-EM structure of a late human pre-40S ribosomal subunit - State F1 Deposited 2020-07-29 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 × 36 PDB declaration: 37-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6ZXE Cryo-EM structure of a late human pre-40S ribosomal subunit - State F2 Deposited 2020-07-29 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 × 36 PDB declaration: 37-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6ZXF Cryo-EM structure of a late human pre-40S ribosomal subunit - State G Deposited 2020-07-29 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 × 36 PDB declaration: 37-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ZXG Cryo-EM structure of a late human pre-40S ribosomal subunit - State H1 Deposited 2020-07-29 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 × 36 PDB declaration: 37-meric
Chain G 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 131 ZN ZINC ION × 3 ASP ASPARTIC ACID × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6ZXH Cryo-EM structure of a late human pre-40S ribosomal subunit - State H2 Deposited 2020-07-29 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 × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded ASP ASPARTIC ACID × 1 MG MAGNESIUM ION × 131 ZN ZINC ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7A09 Structure of a human ABCE1-bound 43S pre-initiation complex - State III Deposited 2020-08-07 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 × 52 PDB declaration: 54-meric
Chain r 1–249（249 aa）
Not recorded ZN ZINC ION × 4 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MET METHIONINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7K5I SARS-COV-2 nsp1 in complex with human 40S ribosome Deposited 2020-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7MQ8 Cryo-EM structure of the human SSU processome, state pre-A1 Deposited 2021-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 71 PDB declaration: 75-meric
Chain L6 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 22 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7MQ9 Cryo-EM structure of the human SSU processome, state pre-A1* Deposited 2021-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 74-meric
Chain L6 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 22 ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.87 Å
7MQA Cryo-EM structure of the human SSU processome, state post-A1 Deposited 2021-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric
Chain L6 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 64 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7QP6 Structure of the human 48S initiation complex in open state (h48S AUG open) Deposited 2022-01-03 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 × 50 PDB declaration: 53-meric
Chain S 1–249（249 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 95 mM KOAc, 3.75 mM Mg(OAc)2, 1 mM ATP, 0.5 mM GTP, 0.25 mM spermidine, 2 mM DTT, 0.4 U/uL RiboLock RNase inhibitor
cryo-EM vitrification conditions Cryogen ETHANE；Cryo-EM grids were prepared by floating home-made continuous carbon on 40 ul sample in the wells of teflon block (custom-made). The sample-covered carbon was then adsorbed to an EM grid.
Resolution 4.70 Å
7QP7 Structure of the human 48S initiation complex in closed state (h48S AUG closed) Deposited 2022-01-03 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 × 48 PDB declaration: 51-meric
Chain S 1–249（249 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 95 mM KOAc, 3.75 mM Mg(OAc)2, 1 mM ATP, 0.5 mM GTP, 0.25 mM spermidine, 2 mM DTT, 0.4 U/uL RiboLock RNase inhibitor
cryo-EM vitrification conditions Cryogen ETHANE；Cryo-EM grids were prepared by floating home-made continuous carbon on 40 ul sample in the wells of teflon block (custom-made). The sample-covered carbon was then adsorbed to an EM grid.
Resolution 3.70 Å
7QVP Human collided disome (di-ribosome) stalled on XBP1 mRNA Deposited 2022-01-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 148 PDB declaration: 162-meric
Chain RG 1–249（249 aa）
Chain SG 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7R4X Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map Deposited 2022-02-09 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 × 34 PDB declaration: 35-meric
Chain G 1–249（249 aa）
Not recorded K POTASSIUM ION × 82 MG MAGNESIUM ION × 88 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.15 Å
7TQL CryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B. Deposited 2022-01-26 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 × 36 PDB declaration: 38-meric
Chain G 1–226（226 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5GP GUANOSINE-5'-MONOPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7WTS Cryo-EM structure of a human pre-40S ribosomal subunit - State UTP14 Deposited 2022-02-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 22 PDB declaration: 23-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7WTT Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (with CK1) Deposited 2022-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric
Chain G 1–249（249 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7WTU Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (without CK1) Deposited 2022-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 33-meric
Chain G 1–249（249 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7WTV Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A2 Deposited 2022-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 35-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7WTW Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A3 Deposited 2022-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7WTX Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-B1 Deposited 2022-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7WTZ Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-B2 Deposited 2022-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7WU0 Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-B3 Deposited 2022-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 35-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7XNX High resolution cry-EM structure of the human 80S ribosome from SNORD127+/+ Kasumi-1 cells Deposited 2022-04-30 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 SG 1–249（249 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 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: 79-meric
Chain SG 1–249（249 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
7ZJW Rabbit 80S ribosome as it decodes the Sec-UGA codon Deposited 2022-04-12 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 × 79 PDB declaration: 86-meric
Chain SR 1–249（249 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 SER SERINE × 1 MG MAGNESIUM ION × 225 K POTASSIUM ION × 18 ZN ZINC ION × 9 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7ZJX Rabbit 80S ribosome programmed with SECIS and SBP2 Deposited 2022-04-12 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 × 77 PDB declaration: 83-meric
Chain SR 1–249（249 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8G5Y mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state) Deposited 2023-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain SG 1–249（249 aa）
Not recorded SPD SPERMIDINE × 13 PUT 1,4-DIAMINOBUTANE × 11 K POTASSIUM ION × 77 MG MAGNESIUM ION × 524 ANM ANISOMYCIN × 1 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 ZN ZINC ION × 8 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.29 Å
8G5Z mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state) Deposited 2023-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 87-meric
Chain SG 1–237（237 aa）
Not recorded SPD SPERMIDINE × 10 K POTASSIUM ION × 45 MG MAGNESIUM ION × 433 ANM ANISOMYCIN × 1 PUT 1,4-DIAMINOBUTANE × 8 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 ZN ZINC ION × 8 PHE PHENYLALANINE × 1 MET METHIONINE × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 ZIY plitidepsin × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8G60 mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state) Deposited 2023-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain SG 1–249（249 aa）
Not recorded SPD SPERMIDINE × 8 PUT 1,4-DIAMINOBUTANE × 10 MG MAGNESIUM ION × 461 ANM ANISOMYCIN × 1 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 K POTASSIUM ION × 10 ZN ZINC ION × 7 PHE PHENYLALANINE × 1 MET METHIONINE × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 ZIY plitidepsin × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.54 Å
8G61 mRNA decoding in human is kinetically and structurally distinct from bacteria (AC state) Deposited 2023-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain SG 1–249（249 aa）
Not recorded PUT 1,4-DIAMINOBUTANE × 4 K POTASSIUM ION × 16 MG MAGNESIUM ION × 326 ANM ANISOMYCIN × 1 SPD SPERMIDINE × 5 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 ZN ZINC ION × 8 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
8G6J mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2) Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain SG 1–249（249 aa）
Not recorded SPD SPERMIDINE × 10 K POTASSIUM ION × 34 MG MAGNESIUM ION × 337 PUT 1,4-DIAMINOBUTANE × 8 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 × 8 PHE PHENYLALANINE × 1 MET METHIONINE × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 YRB (3R,6R,9S,12S,15S,18S,20R,24aR)-6-[(2S)-butan-2-yl]-3,12-bis[(1R)-1-hydroxy-2-methylpropyl]-8,9,11,17,18-pentamethyl-15-[(2S)-2-methylbutyl]hexadecahydropyrido[1,2-a][1,4,7,10,13,16,19]heptaazacyclohenicosine-1,4,7,10,13,16,19(21H)-heptone × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8GLP mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure) Deposited 2023-03-22 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 × 75 PDB declaration: 81-meric
Chain SG 1–249（249 aa）
Not recorded SPD SPERMIDINE × 15 PUT 1,4-DIAMINOBUTANE × 9 K POTASSIUM ION × 152 MG MAGNESIUM ION × 671 ANM ANISOMYCIN × 1 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 ZN ZINC ION × 8 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.67 Å
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 3H 1–249（249 aa）
Not recorded 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 3H 1–249（249 aa）
Not recorded 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
8JDJ Structure of the Human cytoplasmic Ribosome with human tRNA Asp(Q34) and mRNA(GAU) Deposited 2023-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 80-meric
Chain 3 1–249（249 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 mutation/modification 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 3 1–249（249 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 mutation/modification 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 3 1–249（249 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 mutation/modification 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 3 1–249（249 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 SG 1–249（249 aa）
Not recorded 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
8OZ0 Structure of a human 48S translation initiation complex with eIF4F and eIF4A Deposited 2023-05-06 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 × 54 PDB declaration: 57-meric
Chain S 1–249（249 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 89 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8PJ1 Structure of human 48S translation initiation complex in open codon scanning state (48S-1) Deposited 2023-06-22 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 × 51 PDB declaration: 54-meric
Chain S 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 90 ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.40 Å
8PJ2 Structure of human 48S translation initiation complex in AUG recognition state after eIF5-induced GTP hydrolysis by eIF2 (48S-2) Deposited 2023-06-22 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 × 46 PDB declaration: 49-meric
Chain S 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.40 Å
8PJ3 Structure of human 48S translation initiation complex upon transfer of initiator tRNA to eIF5B (48S-3) Deposited 2023-06-22 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 × 51 PDB declaration: 54-meric
Chain S 1–249（249 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 89 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.70 Å
8PJ4 Structure of human 48S translation initiation complex after eIF5 release (48S-4) Deposited 2023-06-22 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 × 50 PDB declaration: 53-meric
Chain S 1–249（249 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 89 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.20 Å
8PJ5 Structure of human 48S translation initiation complex after eIF2 release prior 60S subunit joining (48S-5) Deposited 2023-06-22 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 × 48 PDB declaration: 51-meric
Chain S 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 91 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 2.90 Å
8PJ6 Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and eIF3 (off-pathway) Deposited 2023-06-22 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 × 47 PDB declaration: 50-meric
Chain S 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 2.90 Å
8PPK Bat-Hp-CoV Nsp1 and eIF1 bound to the human 40S small ribosomal subunit Deposited 2023-07-07 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 × 36 PDB declaration: 37-meric
Chain G 1–249（249 aa）
Not recorded UNX UNKNOWN LIGAND × 117 MG MAGNESIUM ION × 111 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.98 Å
8PPL MERS-CoV Nsp1 bound to the human 43S pre-initiation complex Deposited 2023-07-07 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 × 50 PDB declaration: 52-meric
Chain AG 1–249（249 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 116 MET METHIONINE × 1 UNX UNKNOWN LIGAND × 129 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.65 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 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: 79-meric
Chain SG 1–249（249 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
8T4S MERS-CoV Nsp1 protein bound to the Human 40S Ribosomal subunit Deposited 2023-06-09 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 × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 97 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UKB In situ HHT and CHX treated human hibernating state without E-tRNA 80S ribosome Deposited 2023-10-12 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 × 80 PDB declaration: 84-meric
Chain SG 1–237（237 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
8XP2 Cryo-EM structure of the human 40S ribosome with LARP1 Deposited 2024-01-02 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 × 35 PDB declaration: 36-meric
Chain SG 1–249（249 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8XP3 Cryo-EM structure of the human 40S ribosome with LARP1 and LRRC47 Deposited 2024-01-02 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 × 36 PDB declaration: 37-meric
Chain SG 1–249（249 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8XSX Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2 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 SG 1–249（249 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 SG 1–249（249 aa）
Not recorded 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 SG 1–249（249 aa）
Not recorded 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
8XXL Cryo-EM structure of the human 40S ribosome with PDCD4 Deposited 2024-01-18 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 × 35 PDB declaration: 36-meric
Chain SG 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 22 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8XXM Cryo-EM structure of the human 40S ribosome with PDCD4 and eIF3G Deposited 2024-01-18 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 × 36 PDB declaration: 37-meric
Chain SG 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 23 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8XXN Cryo-EM structure of the human 43S ribosome with PDCD4 Deposited 2024-01-18 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 × 49 PDB declaration: 50-meric
Chain SG 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 23 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8Y0W dormant ribosome with eIF5A, eEF2 and SERBP1 Deposited 2024-01-23 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 SG 1–249（249 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 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: 80-meric
Chain SG 1–249（249 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 SG 1–249（249 aa）
Not recorded 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 mutation/modification 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 SG 1–249（249 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
8ZDB Cryo-EM structure of the human ubiquitylated 40S ribosome with RIOK3 Deposited 2024-05-01 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 × 37 PDB declaration: 38-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZDC Cryo-EM structure of the human ubiquitylated pre-40S ribosome with RIOK3 Deposited 2024-05-01 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 × 37 PDB declaration: 38-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8ZDD Cryo-EM structure of the human ubiquitylated pre-40S ribosome with RIOK3 (without NOB1) Deposited 2024-05-01 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 × 36 PDB declaration: 37-meric
Chain G 1–249（249 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9B0P In situ human Hibernating class1 80S ribosome 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 × 80 PDB declaration: 85-meric
Chain SG 1–237（237 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 SG 1–237（237 aa）
Chain sG 1–237（237 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 SG 1–237（237 aa）
Chain sG 1–237（237 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
9BKD The structure of human Pdcd4 bound to the 40S small ribosomal subunit Deposited 2024-04-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain S 1–249（249 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 19 MG MAGNESIUM ION × 88 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9BLN The structure of human Pdcd4 bound to the 40S-eIF4A-eIF3-eIF1 complex Deposited 2024-04-30 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 × 49 PDB declaration: 50-meric
Chain S 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 88 K POTASSIUM ION × 19 SPD SPERMIDINE × 1 ZN ZINC ION × 3 ACY ACETIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 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 SG 1–249（249 aa）
Not recorded 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
9ED0 Human LARP1 bound to the 40S small ribosomal subunit Deposited 2024-11-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded K POTASSIUM ION × 71 MG MAGNESIUM ION × 92 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9FQZ CRYO-EM STRUCTURE OF HCT15 POLYSOMES BOUND TO EEF2, EBP1, AND SERBP1 Deposited 2024-06-17 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 × 79 PDB declaration: 84-meric
Chain SG 1–249（249 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 mutation/modification 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 SG 1–249（249 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
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain SG 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
9I14 CRYO-EM STRUCTURE OF HCT15 POLYSOMES IN HYBRID-PRE STATE Deposited 2025-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain SG 1–249（249 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 mutation/modification 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 SG 1–249（249 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 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 SG 1–249（249 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
9KKF Structure of the human 40S ribosome complexed with HCV IRES and eIF3 Deposited 2024-11-13 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 × 43 PDB declaration: 45-meric
Chain SG 1–249（249 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9KMT Bat SARSr-CoV RaTG15 Nsp1 bound to the Human 40S Ribosomal subunit-State1 Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
9KMU Bat SARSr-CoV RaTG15 Nsp1 bound to the Human 40S Ribosomal subunit-State2 Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
9KMV SARSr-MpCoV-GX Nsp1 bound to the Human 40S Ribosomal subunit-State1 Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
9KMW SARSr-MpCoV-GX Nsp1 bound to the Human 40S Ribosomal subunit-State2 Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.73 Å
9KMX Bat MERSr-CoV NeoCoV Nsp1 bound to the Human 40S Ribosomal subunit-State1 Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
9KMY Bat MERSr-CoV NeoCoV Nsp1 bound to the Human 40S Ribosomal subunit-State2 Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9KMZ Bat MERSr-CoV NL140422 Nsp1 bound to the Human 40S Ribosomal subunit-State1 Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9KN0 Bat MERSr-CoV NL140422 Nsp1 bound to the Human 40S Ribosomal subunit-State2 Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain G 1–249（249 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
9KN5 Structure of the human 40S ribosome complexed with HCV IRES, eIF1A and eIF3 Deposited 2024-11-18 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 × 44 PDB declaration: 46-meric
Chain SG 1–249（249 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9KN6 Structure of the HCV IRES-dependent pre-48S translation initiation complex with eIF1A, eIF5B, and eIF3 Deposited 2024-11-18 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 × 45 PDB declaration: 48-meric
Chain SG 1–249（249 aa）
Not recorded MG MAGNESIUM ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9KRP Structure of the HCV IRES-dependent 48S translation initiation complex with eIF5B and eIF3 Deposited 2024-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain SG 1–249（249 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 9 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 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 mutation/modification 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 SG 1–249（249 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 mutation/modification 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 SG 1–249（249 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 mutation/modification 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 SG 1–249（249 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
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 SG 1–249（249 aa）
Not recorded 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 SG 1–249（249 aa）
Not recorded 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 SG 1–249（249 aa）
Not recorded 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 mutation/modification 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 SG 1–237（237 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 mutation/modification 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 SG 1–237（237 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 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: 85-meric
Chain SG 1–237（237 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 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: 85-meric
Chain SG 1–237（237 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 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 SG 1–237（237 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 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 SG 1–237（237 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 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 SG 1–237（237 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 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 SG 1–237（237 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 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 SG 1–237（237 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 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 SG 1–237（237 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 mutation/modification 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 SG 1–237（237 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 mutation/modification 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 SG 1–237（237 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 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: 85-meric
Chain SG 1–237（237 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 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 SG 1–237（237 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 mutation/modification 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 SG 1–237（237 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 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 SG 1–237（237 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 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: 85-meric
Chain SG 1–237（237 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 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 SG 1–237（237 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 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 SG 1–237（237 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 mutation/modification 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 SG 1–237（237 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 mutation/modification 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 SG 1–237（237 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 mutation/modification 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 SG 1–237（237 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 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 SG 1–237（237 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 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: 85-meric
Chain SG 1–237（237 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 mutation/modification 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 SG 1–237（237 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 mutation/modification 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 SG 1–237（237 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 mutation/modification 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 SG 1–237（237 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 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: 84-meric
Chain SG 1–237（237 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
9PA7 In situ human 80S consensus ribosome with EBP1 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 × 81 PDB declaration: 87-meric
Chain SG 1–237（237 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 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: 84-meric
Chain SG 1–237（237 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 mutation/modification 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 SG 1–237（237 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
9QLO NMT1-NAC bound human RNC with full length ARF1 - State 1 Deposited 2025-03-21 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 × 82 PDB declaration: 88-meric
Chain SG 1–249（249 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 mutation/modification 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 SG 1–249（249 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 mutation/modification 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 SG 1–249（249 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 RG 1–249（249 aa）
Chain SG 1–249（249 aa）
Not recorded 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 SG 1–249（249 aa）
Not recorded 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 80-meric
Chain SG 1–249（249 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain SG 1–249（249 aa）
Not recorded 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 73 PDB declaration: 80-meric
Chain SG 1–249（249 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 mutation/modification 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 SG 1–249（249 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 mutation/modification 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 SG 1–249（249 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 mutation/modification 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 SG 1–249（249 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 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: 87-meric
Chain SG 1–249（249 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 SG 1–249（249 aa）
Not recorded 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 SG 1–249（249 aa）
Not recorded 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
9SYR Human quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatD Deposited 2025-10-13 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 × 80 PDB declaration: 86-meric
Chain Sy 1–249（249 aa）
Not recorded ZN ZINC ION × 10 COA COENZYME A × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.55 Å

203 other PDB entries and 208 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RS6_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–16； UniProt 129–144

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 6f4q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6f4q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6f4q
Deposition date deposition_date2017-11-29
Structure title titleHuman JMJD5 (Q275C) in complex with Mn(II), NOG and RPS6-A138C (129-144) (complex-2)
Keywords keywords;OXIDOREDUCTASE, NON-HEME, IRON, 2-OXOGLUTARATE, DIOXYGENASE, JMJC, JMJC DOMAIN, Lysine-specific demethylase 8, JmjC domain-containing protein 5, Arginyl C-3 Hydroxylase, JMJD5, KDM8, OXYGENASE, HYPOXIA, DNA-BINDING, METAL-BINDING, TRANSLATION, DSBH, FACIAL TRIAD, CYTOPLASM, JMJC HYDROXYLASE, JMJC DEMETHYLASE, KDMS, POST-TRANSLATIONAL MODIFICATIONS, PTM, BETA-HYDROXYLATION, HYDROXYLATION, ARGININE HYDROXYLATION, RCC1 domain-containing protein 1, RCCD1, Regulator of chromosome condensation, 40S ribosomal protein S6, RPS6, RIBOSOME BIOGENESIS, TRANSCRIPTION, EPIGENETIC REGULATION, SIGNALING, DEVELOPMENT, CELL STRUCTURE, TRANSCRIPTION ACTIVATOR/INHIBITOR, PHOSPHORYLATION, CANCER, POLYMORPHISM ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.81 Å
Radius of gyration Rg (electron density) rg_electron17.61 Å
Forward intensity I(0) i012927300.00
Molecular weight molecular_weight27548.0 kDa
Excluded volume excluded_volume34670 ų
Envelope volume envelope_volume39051 ų
Hydration-shell volume shell_volume18377 ų
Envelope diameter envelope_diameter60.0 Å
Shell Rg shell_rg24.04 Å
Envelope Rg envelope_rg17.92 Å
Shape Rg shape_rg17.59 Å
Total Rg total_rg18.63 Å
Total atoms total_atoms3818
Residues n_residues237
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax59.2 Å
Rg (real space) rg_real18.70 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real1.2930e+07
I(0) uncertainty (real space) i0_real_error1.5680e+05
Rg (reciprocal space) rg_reciprocal18.72 Å
I(0) (reciprocal space) i0_reciprocal12930000.0000
Solution quality estimate total_estimate0.8961
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.7 Å
Skewness Skewness skewness0.180
Kurtosis Kurtosis kurtosis-0.423
Angular range angular_range— – 0.4250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3317000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.990
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id6f4qA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
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8. Citations (1)

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9. Files and Curves (10)