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4cco

60S ribosomal protein L8 histidine hydroxylase (NO66 S373C) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G214C) peptide fragment (complex-3)

Method: X-RAY DIFFRACTION Dmax: 117.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66

HOMO SAPIENS

UniProt Q9H6W3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 183–641 Chain B； UniProt 183–641 Fragment：CATALYTIC DOMAIN, RESIDUES 183-641 60S RIBOSOMAL PROTEIN L8 × 4 （P62917） MN MANGANESE (II) ION × 4 OGA N-OXALYLGLYCINE × 4 EDO 1,2-ETHANEDIOL × 10 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；VAPOR DIFFUSION, SITTING DROP 0.1M BIS-TRIS PROPANE PH 7.4, 0.36M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K Resolution 2.30 Å R-free 0.225

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 4CCO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4CCJ 60S ribosomal protein L8 histidine hydroxylase (NO66) in apo form Deposited 2013-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain B 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain C 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain D 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Mutation：YES Mutation：YES Mutation：YES Mutation：YES EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；NAPOR DIFFUSION, SITTING DROP 0.1M BIS-TRIS PROPANE PH 5.6-6.5, 0.5-0.7M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K
Resolution 2.15 Å R-free 0.210
4CCK 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II) and N-oxalylglycine (NOG) Deposited 2013-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain B 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain C 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain D 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Mutation：YES Mutation：YES Mutation：YES Mutation：YES MN MANGANESE (II) ION × 4 OGA N-OXALYLGLYCINE × 4 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；VAPOR DIFFUSION, SITTING DROP 0.1M BIS-TRIS PROPANE PH 5.6-6.5, 0.5-0.7M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K
Resolution 2.15 Å R-free 0.197
4CCM 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1) Deposited 2013-10-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain B 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Not recorded MN MANGANESE (II) ION × 4 OGA N-OXALYLGLYCINE × 4 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M BIS-TRIS PROPANE PH 6.8, 0.25M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K VAPOR DIFFUSION, SITTING DROP
Resolution 2.51 Å R-free 0.236
4CCN 60S ribosomal protein L8 histidine hydroxylase (NO66 L299C/C300S) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-2) Deposited 2013-10-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Chain B 183–641（459 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 183-641
Not recorded MN MANGANESE (II) ION × 4 OGA N-OXALYLGLYCINE × 4 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；VAPOR DIFFUSION, SITTING DROP 0.1M BIS-TRIS PROPANE PH 7.4, 0.4M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K
Resolution 2.23 Å R-free 0.248
4DIQ Crystal Structure of human NO66 Deposited 2012-01-31 Different construct 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 167–641（475 aa） Fragment：UNP residues 161-641
Chain B 167–641（475 aa） Fragment：UNP residues 161-641
Not recorded NI NICKEL (II) ION × 2 PD2 PYRIDINE-2,4-DICARBOXYLIC ACID × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.05M (NH4)2SO4, 0.05M BIS-TRIS pH 6.5, 30% pentaerythritol ethoxylate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.40 Å R-free 0.230
4DIQ Crystal Structure of human NO66 Deposited 2012-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 167–641（475 aa） Fragment：UNP residues 161-641
Chain B 167–641（475 aa） Fragment：UNP residues 161-641
Not recorded NI NICKEL (II) ION × 4 PD2 PYRIDINE-2,4-DICARBOXYLIC ACID × 4 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.05M (NH4)2SO4, 0.05M BIS-TRIS pH 6.5, 30% pentaerythritol ethoxylate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.40 Å R-free 0.230
4E4H Crystal structure of Histone Demethylase NO66 Deposited 2012-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 183–641（459 aa） Fragment：UNP RESIDUES 183-641
Chain B 183–641（459 aa） Fragment：UNP RESIDUES 183-641
Chain C 183–641（459 aa） Fragment：UNP RESIDUES 183-641
Chain D 183–641（459 aa） Fragment：UNP RESIDUES 183-641
Not recorded FE FE (III) ION × 4 ACT ACETATE ION × 1 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；200mM (NH4)2SO4, 100mM Tris-HCl, 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.28 Å R-free 0.252
4Y33 Crystal of NO66 in complex with Ni(II)and N-oxalylglycine (NOG) Deposited 2015-02-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 176–641（466 aa） Fragment：UNP RESIDUES 176-641
Chain B 176–641（466 aa） Fragment：UNP RESIDUES 176-641
Chain C 176–641（466 aa） Fragment：UNP RESIDUES 176-641
Chain D 176–641（466 aa） Fragment：UNP RESIDUES 176-641
Not recorded NI NICKEL (II) ION × 4 OGA N-OXALYLGLYCINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；15%(v/v) ethanol, imidazole pH8.0, 0.2M magnesium chloride
Resolution 2.70 Å R-free 0.274
4Y3O Crystal structure of Ribosomal oxygenase NO66 in complex with substrate Rpl8 peptide and Ni(II) and cofactor N-oxalyglycine Deposited 2015-02-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 176–641（466 aa） Fragment：UNP RESIDUES 176-641
Chain B 176–641（466 aa） Fragment：UNP RESIDUES 176-641
Not recorded NI NICKEL (II) ION × 2 OGA N-OXALYLGLYCINE × 2 GOL GLYCEROL × 3 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.1 M Imidazole pH 6.5, 0.5 M Sodium acetate trihydrate
Resolution 2.20 Å R-free 0.262
4Y4R Crystal structure of ribosomal oxygenase NO66 dimer mutant Deposited 2015-02-11 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 176–525（350 aa） Fragment：UNP RESIDUES 176-525, 541-641
Chain A 541–641（101 aa） Fragment：UNP RESIDUES 176-525, 541-641
Chain B 176–525（350 aa） Fragment：UNP RESIDUES 176-525, 541-641
Chain B 541–641（101 aa） Fragment：UNP RESIDUES 176-525, 541-641
Not recorded NI NICKEL (II) ION × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1.0M ammonium monohydric phosphate, 0.1M acetate pH4.5
Resolution 3.30 Å R-free 0.271

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NO66_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–460； UniProt 183–641 Author chain B； PDBConstruct 2–460； UniProt 183–641

60S RIBOSOMAL PROTEIN L8

OrganismNot specified

UniProt P62917

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain C； UniProt 205–224 Chain D； UniProt 205–224 Fragment：RESIDUES 205-239 Mutation：YES BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66 × 4 （Q9H6W3） MN MANGANESE (II) ION × 4 OGA N-OXALYLGLYCINE × 4 EDO 1,2-ETHANEDIOL × 10 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；VAPOR DIFFUSION, SITTING DROP 0.1M BIS-TRIS PROPANE PH 7.4, 0.36M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K Resolution 2.30 Å R-free 0.225

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 4CCO 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 LA 1–257（257 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain BA 1–257（257 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.70 Å
4CCM 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1) Deposited 2013-10-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 205–239（35 aa） Fragment：RESIDUES 205-239
Chain D 205–239（35 aa） Fragment：RESIDUES 205-239
Mutation：YES Mutation：YES MN MANGANESE (II) ION × 4 OGA N-OXALYLGLYCINE × 4 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M BIS-TRIS PROPANE PH 6.8, 0.25M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K VAPOR DIFFUSION, SITTING DROP
Resolution 2.51 Å R-free 0.236
4CCN 60S ribosomal protein L8 histidine hydroxylase (NO66 L299C/C300S) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-2) Deposited 2013-10-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 205–239（35 aa） Fragment：RESIDUES 205-239
Chain D 205–239（35 aa） Fragment：RESIDUES 205-239
Mutation：YES Mutation：YES MN MANGANESE (II) ION × 4 OGA N-OXALYLGLYCINE × 4 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；VAPOR DIFFUSION, SITTING DROP 0.1M BIS-TRIS PROPANE PH 7.4, 0.4M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K
Resolution 2.23 Å R-free 0.248
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 LA 1–257（257 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 84 PDB declaration: 89-meric
Chain CA 1–257（257 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
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 AA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 326 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-KOH, PH 7.5, 100 MM KCL, 1.5 MM MGCL2, 0.5 MM SPERMIDINE, 0.04 MM SPERMINE, 1 MM DTT；pH 7.5；20 MM HEPES-KOH, PH 7.5, 100 MM KCL, 1.5 MM MGCL2, 0.5 MM SPERMIDINE, 0.04 MM SPERMINE, 1 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 93, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT FOR 2-4 SECONDS BEFORE PLUNGING,
Resolution 3.50 Å
5LKS Structure-function insights reveal the human ribosome as a cancer target for antibiotics Deposited 2016-07-23 Different construct Different 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 LA 1–257（257 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 224 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
5T2C CryoEM structure of the human ribosome at 3.6 Angstrom resolution Deposited 2016-08-23 Different construct Different 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 D 1–257（257 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6IP5 Cryo-EM structure of the CMV-stalled human 80S ribosome (Structure ii) Deposited 2018-11-02 Different construct Different 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 1D 1–257（257 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain 1D 1–257（257 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 1D 1–257（257 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6LQM Cryo-EM structure of a pre-60S ribosomal subunit - state C Deposited 2020-01-14 Different construct Different 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 m 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 251 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
6LSR Cryo-EM structure of a pre-60S ribosomal subunit - state B Deposited 2020-01-20 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 × 45 PDB declaration: 48-meric
Chain m 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 246 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
6LSS Cryo-EM structure of a pre-60S ribosomal subunit - state preA Deposited 2020-01-20 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 × 45 PDB declaration: 48-meric
Chain m 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 250 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
6LU8 Cryo-EM structure of a human pre-60S ribosomal subunit - state A Deposited 2020-01-26 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 × 47 PDB declaration: 50-meric
Chain m 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 247 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 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 A 2–253（252 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 A 2–253（252 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 AA 1–257（257 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 A 2–253（252 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 AA 2–249（248 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 A 2–253（252 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 A 2–253（252 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 LA 2–249（248 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
6W6L Cryo-EM structure of the human ribosome-TMCO1 translocon Deposited 2020-03-17 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 × 49 PDB declaration: 54-meric
Chain A 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 28 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Two filter papers were added to each arm, 2.5 microliters of sample were added to the grids, and 0.5 seconds of drain time was allowed before vitrification.
Resolution 3.84 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 LA 2–249（248 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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 160 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6Y6X Tetracenomycin X bound to the human ribosome Deposited 2020-02-27 Different construct Different 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: 46-meric
Chain LA 2–249（248 aa）
Not recorded MG MAGNESIUM ION × 229 OCW Tetracenomycin X × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6Z6L Cryo-EM structure of human CCDC124 bound to 80S ribosomes Deposited 2020-05-28 Different construct Different 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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6ZM7 SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex Deposited 2020-07-01 Different construct Different 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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 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
7BHP Cryo-EM structure of the human Ebp1 - 80S ribosome Deposited 2021-01-11 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 × 41 PDB declaration: 45-meric
Chain LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 41 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7F5S human delta-METTL18 60S ribosome Deposited 2021-06-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 279 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
7OW7 EIF6-bound large subunit of the human ribosome Deposited 2021-06-16 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 × 40 PDB declaration: 43-meric
Chain D 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 223 ZN ZINC ION × 5 K POTASSIUM ION × 153 NA SODIUM ION × 4 BR BROMIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
7UN3 Complex of UBE2O with NAP1L1 and ubiquitylated uL2 Deposited 2022-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–257（257 aa）
Chain D 1–257（257 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7XNX High resolution cry-EM structure of the human 80S ribosome from SNORD127+/+ Kasumi-1 cells Deposited 2022-04-30 Different construct Different 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 LA 1–257（257 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 LA 1–257（257 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
8A3D Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound Deposited 2022-06-08 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 × 42 PDB declaration: 45-meric
Chain D 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 229 K POTASSIUM ION × 155 NA SODIUM ION × 2 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 SPM SPERMINE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；30 seconds 'wait' time
Resolution 1.67 Å
8FKZ Human nucleolar pre-60S ribosomal subunit (State G) Deposited 2022-12-21 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 × 48 PDB declaration: 51-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 64 ZN ZINC ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 3.04 Å
8FL2 Human nuclear pre-60S ribosomal subunit (State I1) Deposited 2022-12-21 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 × 61 PDB declaration: 65-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 100 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.67 Å
8FL3 Human nuclear pre-60S ribosomal subunit (State I2) Deposited 2022-12-21 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 × 60 PDB declaration: 63-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 100 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.53 Å
8FL4 Human nuclear pre-60S ribosomal subunit (State I3) Deposited 2022-12-21 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 × 59 PDB declaration: 62-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 99 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.89 Å
8FL6 Human nuclear pre-60S ribosomal subunit (State J1) Deposited 2022-12-21 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 × 52 PDB declaration: 56-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 88 ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.62 Å
8FL7 Human nuclear pre-60S ribosomal subunit (State J2) Deposited 2022-12-21 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 × 51 PDB declaration: 54-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 88 ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.55 Å
8FL9 Human nuclear pre-60S ribosomal subunit (State J3) Deposited 2022-12-21 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 × 47 PDB declaration: 50-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 88 ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.75 Å
8FLA Human nuclear pre-60S ribosomal subunit (State K1) Deposited 2022-12-21 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 × 52 PDB declaration: 56-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 88 ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.63 Å
8FLB Human nuclear pre-60S ribosomal subunit (State K2) Deposited 2022-12-21 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 × 51 PDB declaration: 54-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 88 ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.55 Å
8FLC Human nuclear pre-60S ribosomal subunit (State K3) Deposited 2022-12-21 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 × 47 PDB declaration: 50-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 88 ZN ZINC ION × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.76 Å
8FLD Human nuclear pre-60S ribosomal subunit (State L1) Deposited 2022-12-21 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 × 50 PDB declaration: 54-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the Vitrobot.
Resolution 2.58 Å
8FLE Human nuclear pre-60S ribosomal subunit (State L2) Deposited 2022-12-21 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 × 49 PDB declaration: 52-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the Vitrobot.
Resolution 2.48 Å
8FLF Human nuclear pre-60S ribosomal subunit (State L3) Deposited 2022-12-21 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 × 45 PDB declaration: 48-meric
Chain SF 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the Vitrobot.
Resolution 2.65 Å
8IDT human nuclear pre-60S ribosomal particle - State G 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 × 48 PDB declaration: 51-meric
Chain m 1–257（257 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 K POTASSIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8IDY human nuclear pre-60S ribosomal particle - State F 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 × 51 PDB declaration: 54-meric
Chain m 1–257（257 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8IE3 human nuclear pre-60S ribosomal particle - State E 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 × 45 PDB declaration: 48-meric
Chain m 1–257（257 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 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 1D 1–257（257 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 1D 1–257（257 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
8INE human nuclear pre-60S ribosomal particle - State G' Deposited 2023-03-09 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 × 54 PDB declaration: 58-meric
Chain m 1–257（257 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8INF human nuclear pre-60S ribosomal particle - State F' Deposited 2023-03-09 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 × 57 PDB declaration: 61-meric
Chain m 1–257（257 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8INK human nuclear pre-60S ribosomal particle - State D Deposited 2023-03-10 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 × 50 PDB declaration: 53-meric
Chain m 1–257（257 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8IPD human nuclear pre-60S ribosomal particle - State C Deposited 2023-03-14 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 × 49 PDB declaration: 52-meric
Chain m 1–257（257 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8IPX human nuclear pre-60S ribosomal particle - State C' Deposited 2023-03-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain m 1–257（257 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
8IPY human nuclear pre-60S ribosomal particle - State D' Deposited 2023-03-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric
Chain m 1–257（257 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8IR1 human nuclear pre-60S ribosomal particle - State A Deposited 2023-03-17 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 × 50 PDB declaration: 53-meric
Chain m 1–257（257 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8IR3 human nuclear pre-60S ribosomal particle - State B' Deposited 2023-03-17 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 × 55 PDB declaration: 59-meric
Chain m 1–257（257 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 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 G 1–257（257 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 G 1–257（257 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 G 1–257（257 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 G 1–257（257 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 LA 1–257（257 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
8OHD 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native) Deposited 2023-03-21 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 × 47 PDB declaration: 50-meric
Chain LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 220 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8OJ0 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native) Deposited 2023-03-23 Different construct Different 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 LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 220 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OJ5 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution) Deposited 2023-03-23 Different construct Different 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 LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 220 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8OJ8 60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native) Deposited 2023-03-24 Different construct Different 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 LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 220 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8QFD UFL1 E3 ligase bound 60S ribosome Deposited 2023-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain A 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 161 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25 mM HEPES pH 7.5, 50 mM KCl, 5 mM MgCl2, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8QOI Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical modifications and ions in RNA Deposited 2023-09-29 Different construct Different 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 LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 292 K POTASSIUM ION × 108 SPD SPERMIDINE × 2 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；Titan Krios sample is prepared with Sodium cacodylate buffer. CryoARM 300 sample is prepared with Hepes buffer.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8QYX Human 60S ribosomal subunit Deposited 2023-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain D2 1–257（257 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 186 PUT 1,4-DIAMINOBUTANE × 7 K POTASSIUM ION × 46 ZN ZINC ION × 5 SPD SPERMIDINE × 7 SPM SPERMINE × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.78 Å
8RL2 Human pre-60S - State 5 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 × 49 PDB declaration: 52-meric
Chain LA 1–257（257 aa）
Not recorded ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.84 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 LA 2–249（248 aa）
Not recorded MG MAGNESIUM ION × 255 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 WV3 4-{(2R)-2-[(1R,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8XSX Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2 Deposited 2024-01-10 Different construct Different 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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 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
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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9B0P In situ human Hibernating class1 80S ribosome Deposited 2024-03-12 Different construct Different 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 LA 2–249（248 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 LA 2–249（248 aa）
Chain lA 2–249（248 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 LA 2–249（248 aa）
Chain lA 2–249（248 aa）
Not recorded ZN ZINC ION × 12 MG MAGNESIUM ION × 510 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9C3H Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site. Deposited 2024-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain LD 1–257（257 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 326 K POTASSIUM ION × 94 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
9FQZ CRYO-EM STRUCTURE OF HCT15 POLYSOMES BOUND TO EEF2, EBP1, AND SERBP1 Deposited 2024-06-17 Different construct Different 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 LA 1–257（257 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 LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 232 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
9GMO eIF6-bound pre-60S large ribosomal subunit incorporating mutant uL16 Deposited 2024-08-29 Different construct Different 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: 46-meric
Chain D 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 227 K POTASSIUM ION × 155 NA SODIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.59 Å
9GUL Structure of FLuc-XBP1u+ stalled human 60S ribosome nascent chain complex Deposited 2024-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 46-meric
Chain LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 284 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9GY4 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map) Deposited 2024-10-01 Different construct Different 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: 55-meric
Chain a 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 219 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9I14 CRYO-EM STRUCTURE OF HCT15 POLYSOMES IN HYBRID-PRE STATE Deposited 2025-01-15 Different construct Different 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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9KZU Cryo-EM structure of the HCV IRES-dependently initiated CMV-stalled 80S ribosome (non-rotated state) in complexed with eIF3 Deposited 2024-12-11 Different construct Different 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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 aa）
Not recorded MG MAGNESIUM ION × 291 ZN ZINC ION × 6 A1L8F (1S,13S,15S,16S)-16-methoxy-5,7-dioxa-12-azapentacyclo[10.6.1.02,10.04,8.013,18]nonadeca-2,4(8),9,17-tetraen-15-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9N9J Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon Deposited 2025-02-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 70-meric
Chain LA 1–257（257 aa）
Not recorded ELU phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate × 1 MG MAGNESIUM ION × 226 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；HEPES buffer was adjusted to pH 7.4 with potassium hydroxide.
cryo-EM vitrification conditions Cryogen ETHANE；Three microliters of affinity-purified RTCs were applied to the grid, incubated for 60 seconds, blotted for 7 seconds, drained for 0.5 seconds, and frozen in liquid nitrogen-cooled ethane.
Resolution 3.20 Å
9O3V Human 80S ribosome stalled on MYC nascent chain Deposited 2025-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.77 Å
9P9J In situ human 60S ribosome Deposited 2025-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 44-meric
Chain LA 2–249（248 aa）
Not recorded MG MAGNESIUM ION × 191 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
9P9K In situ human 60S ribosome with EIF6 Deposited 2025-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric
Chain LA 2–249（248 aa）
Not recorded MG MAGNESIUM ION × 191 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9PA7 In situ human 80S consensus ribosome with EBP1 Deposited 2025-06-25 Different construct Different 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 LA 2–249（248 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 LA 2–249（248 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 LA 2–249（248 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
9QIW Human pre-60S - State 3 Deposited 2025-03-17 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 × 48 PDB declaration: 51-meric
Chain LA 1–257（257 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 aa）
Chain MA 1–257（257 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 830 ZN ZINC ION × 7 ANM ANISOMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.35 Å
9RU7 WT-HEK 80S ribosome bound to Kozak mRNA (WT-Kozak) Deposited 2025-07-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LA 1–252（252 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 17 MG MAGNESIUM ION × 74 C CYTIDINE-5'-MONOPHOSPHATE × 2 NA SODIUM ION × 7 ZN ZINC ION × 5 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9RU8 WT-HEK 80S ribosome bound to TISU mRNA (WT-TISU) Deposited 2025-07-03 Different construct Different 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 LA 1–257（257 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9RU9 RPS26dC HEK mutant 80S ribosome bound to Kozak mRNA (RPS26dC-Kozak) Deposited 2025-07-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain LA 1–257（257 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.97 Å
9RUA RPS26dC HEK mutant 80S ribosome bound to TISU mRNA (RPS26dC-TISU) Deposited 2025-07-03 Different construct Different 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 LA 1–257（257 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.90 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 LA 1–254（254 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 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 LA 1–257（257 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 151 MG MAGNESIUM ION × 225 NA SODIUM ION × 35 SPD SPERMIDINE × 19 PUT 1,4-DIAMINOBUTANE × 9 ZN ZINC ION × 7 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9SPI CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINE Deposited 2025-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 83-meric
Chain LA 1–257（257 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PUT 1,4-DIAMINOBUTANE × 8 SPD SPERMIDINE × 18 MG MAGNESIUM ION × 195 K POTASSIUM ION × 75 ZN ZINC ION × 7 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
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 La 1–257（257 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

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View Construct and Data Evidence
UniProt name RL8_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–20； UniProt 205–224 Author chain D； PDBConstruct 1–20； UniProt 205–224

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 4cco

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4cco
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4cco
Deposition date deposition_date2013-10-23
Structure title title60S ribosomal protein L8 histidine hydroxylase (NO66 S373C) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G214C) peptide fragment (complex-3)
Keywords keywords;OXIDOREDUCTASE, NON-HEME, IRON-BINDING, DSBH, 2-OXOGLUTARATE, DIOXYGENASE, JMJC DOMAIN, RIBOSOME BIOGENESIS, NUCLEAR PROTEIN, RPL8, BETA-HYDROXYLATION, TRANSCRIPTION AND EPIGENETIC REGULATION, SIGNALING ;; 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_guinier36.76 Å
Radius of gyration Rg (electron density) rg_electron36.30 Å
Forward intensity I(0) i0176125000.00
Molecular weight molecular_weight106750.0 kDa
Excluded volume excluded_volume133120 ų
Envelope volume envelope_volume175520 ų
Hydration-shell volume shell_volume39901 ų
Envelope diameter envelope_diameter113.7 Å
Shell Rg shell_rg43.52 Å
Envelope Rg envelope_rg35.73 Å
Shape Rg shape_rg36.29 Å
Total Rg total_rg36.79 Å
Total atoms total_atoms7524
Residues n_residues941
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 dmax117.5 Å
Rg (real space) rg_real36.78 Å
Rg uncertainty (real space) rg_real_error0.92 Å
I(0) (real space) i0_real1.7610e+08
I(0) uncertainty (real space) i0_real_error2.7910e+06
Rg (reciprocal space) rg_reciprocal36.78 Å
I(0) (reciprocal space) i0_reciprocal176100000.0000
Solution quality estimate total_estimate0.8930
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary32.8 Å
Skewness Skewness skewness0.206
Kurtosis Kurtosis kurtosis-0.799
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33790000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.936
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id4ccoA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
Domain ID domain_id4ccoA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1500 — JmjC domain-containing ribosomal oxygenase (ROX), dimer domain
Domain ID domain_id4ccoA03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily40 —
Domain ID domain_id4ccoB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
Domain ID domain_id4ccoB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1500 — JmjC domain-containing ribosomal oxygenase (ROX), dimer domain
Domain ID domain_id4ccoB03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily40 —
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8. Citations (2)

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9. Files and Curves (10)