8qfc

UFL1 E3 ligase bound 60S ribosome

Method: ELECTRON MICROSCOPY D_max: 222.9 Å Quality: REASONABLE

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

60S ribosomal protein L10a

Homo sapiens

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–217	Not recorded	E3 UFM1-protein ligase 1 × 1 （O94874） CDK5 regulatory subunit-associated protein 3 × 1 （Q96JB5） DDRGK domain-containing protein 1 × 1 （Q96HY6） Ubiquitin-fold modifier 1 × 1 （A0A8C2YGR4）	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 3.20 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8QFC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4UG0 STRUCTURE OF THE HUMAN 80S RIBOSOME Deposited 2015-03-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 89-meric	Chain Lz 1–217（217 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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 84 PDB declaration: 89-meric	Chain Cz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric	Chain Au 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric	Chain Lz 1–217（217 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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric	Chain l 1–217（217 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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric	Chain 2l 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric	Chain A 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric	Chain A 1–217（217 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
6LU8 Cryo-EM structure of a human pre-60S ribosomal subunit - state A Deposited 2020-01-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain A 1–217（217 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
6OLG Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA) Deposited 2019-04-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric	Chain Au 1–217（217 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
6QZP High-resolution cryo-EM structure of the human 80S ribosome Deposited 2019-03-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric	Chain Lz 1–217（217 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
6Y6X Tetracenomycin X bound to the human ribosome Deposited 2020-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 83 PDB declaration: 88-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric	Chain Lz 1–217（217 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
8FKT Human nucleolar pre-60S ribosomal subunit (State C1) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain BB 1–217（217 aa）	Not recorded	MG MAGNESIUM ION × 64 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 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 2.81 Å
8FKU Human nucleolar pre-60S ribosomal subunit (State C2) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain BB 1–217（217 aa）	Not recorded	MG MAGNESIUM ION × 58 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 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 2.82 Å
8FKV Human nucleolar pre-60S ribosomal subunit (State D1) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric	Chain BB 1–217（217 aa）	Not recorded	MG MAGNESIUM ION × 65 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 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 2.47 Å
8FKW Human nucleolar pre-60S ribosomal subunit (State D2) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain BB 1–217（217 aa）	Not recorded	MG MAGNESIUM ION × 59 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 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 2.50 Å
8FKX Human nucleolar pre-60S ribosomal subunit (State E) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain BB 1–217（217 aa）	Not recorded	MG MAGNESIUM ION × 61 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 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 2.59 Å
8FKY Human nucleolar pre-60S ribosomal subunit (State F) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 59-meric	Chain BB 1–217（217 aa）	Not recorded	MG MAGNESIUM ION × 70 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 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 2.67 Å
8FL2 Human nuclear pre-60S ribosomal subunit (State I1) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 65-meric	Chain BB 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 60 PDB declaration: 63-meric	Chain BB 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 62-meric	Chain BB 1–217（217 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
8G5Y mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state) Deposited 2023-02-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric	Chain Lz 1–217（217 aa）	Not recorded	SPD SPERMIDINE × 13 PUT 1,4-DIAMINOBUTANE × 11 K POTASSIUM ION × 77 MG MAGNESIUM ION × 524 ANM ANISOMYCIN × 1 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 ZN ZINC ION × 8 MET METHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.29 Å
8G60 mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state) Deposited 2023-02-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric	Chain Lz 1–217（217 aa）	Not recorded	SPD SPERMIDINE × 8 PUT 1,4-DIAMINOBUTANE × 10 MG MAGNESIUM ION × 461 ANM ANISOMYCIN × 1 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 K POTASSIUM ION × 10 ZN ZINC ION × 7 PHE PHENYLALANINE × 1 MET METHIONINE × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 ZIY plitidepsin × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å
8G61 mRNA decoding in human is kinetically and structurally distinct from bacteria (AC state) Deposited 2023-02-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric	Chain Lz 1–217（217 aa）	Not recorded	PUT 1,4-DIAMINOBUTANE × 4 K POTASSIUM ION × 16 MG MAGNESIUM ION × 326 ANM ANISOMYCIN × 1 SPD SPERMIDINE × 5 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 ZN ZINC ION × 8 MET METHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
8G6J mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2) Deposited 2023-02-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric	Chain Lz 1–217（217 aa）	Not recorded	SPD SPERMIDINE × 10 K POTASSIUM ION × 34 MG MAGNESIUM ION × 337 PUT 1,4-DIAMINOBUTANE × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 ZN ZINC ION × 8 PHE PHENYLALANINE × 1 MET METHIONINE × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 YRB (3R,6R,9S,12S,15S,18S,20R,24aR)-6-[(2S)-butan-2-yl]-3,12-bis[(1R)-1-hydroxy-2-methylpropyl]-8,9,11,17,18-pentamethyl-15-[(2S)-2-methylbutyl]hexadecahydropyrido[1,2-a][1,4,7,10,13,16,19]heptaazacyclohenicosine-1,4,7,10,13,16,19(21H)-heptone × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8IDY human nuclear pre-60S ribosomal particle - State F Deposited 2023-02-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric	Chain t 1–217（217 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
8IFD Dibekacin-added human 80S ribosome Deposited 2023-02-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric	Chain 2l 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric	Chain 2l 1–217（217 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
8INF human nuclear pre-60S ribosomal particle - State F' Deposited 2023-03-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 61-meric	Chain q 1–217（217 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
8K2C Cryo-EM structure of the human 80S ribosome with Tigecycline Deposited 2023-07-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain Lz 1–217（217 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
8UKB In situ HHT and CHX treated human hibernating state without E-tRNA 80S ribosome Deposited 2023-10-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain Lz 1–217（217 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
8Y0W dormant ribosome with eIF5A, eEF2 and SERBP1 Deposited 2024-01-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric	Chain Lz 1–217（217 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
8YOP Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline Deposited 2024-03-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-meric	Chain Lz 1–217（217 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric	Chain Lz 1–217（217 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 conditions	Assembly 1 Protein–RNA Heteromer；Protein × 160 PDB declaration: 172-meric	Chain Lz 1–217（217 aa） Chain lz 1–217（217 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 conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 158 PDB declaration: 171-meric	Chain Lz 1–217（217 aa） Chain lz 1–217（217 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
9GY4 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map) Deposited 2024-10-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric	Chain Lz 1–217（217 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
9I2E NMT1-NAC bound human ribosome (combined translational states) Deposited 2025-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric	Chain Lz 1–217（217 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
9N9J Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon Deposited 2025-02-10	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 70-meric	Chain Lz 1–217（217 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
9RPV Structure of the ZAK-bound human disome Deposited 2025-06-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 168-meric	Chain Ms 1–217（217 aa）	Not recorded	MG MAGNESIUM ION × 830 ZN ZINC ION × 7 ANM ANISOMYCIN × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.35 Å

53 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL10A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–217； UniProt 1–217

E3 UFM1-protein ligase 1

Homo sapiens

UniProt O94874

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain B； UniProt 1–794	Not recorded	60S ribosomal protein L10a × 1 （P62906） CDK5 regulatory subunit-associated protein 3 × 1 （Q96JB5） DDRGK domain-containing protein 1 × 1 （Q96HY6） Ubiquitin-fold modifier 1 × 1 （A0A8C2YGR4）	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 3.20 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8QFC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8B9X Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1 Deposited 2022-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–200（174 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Sodium acetate trihydrate Ammonium tartrate dibasic	Resolution 3.07 Å R-free 0.272
8B9X Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1 Deposited 2022-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–200（174 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Sodium acetate trihydrate Ammonium tartrate dibasic	Resolution 3.07 Å R-free 0.272
8C0D UFL1/DDRGK1 bound to UFC1 Deposited 2022-12-16	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–179（179 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；0.1M HEPES, 1.03M Li2SO4	Resolution 2.56 Å R-free 0.286
8C0D UFL1/DDRGK1 bound to UFC1 Deposited 2022-12-16	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–179（179 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；0.1M HEPES, 1.03M Li2SO4	Resolution 2.56 Å R-free 0.286
8OHD 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native) Deposited 2023-03-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain A 1–794（794 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain A 1–794（794 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric	Chain A 1–794（794 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain A 1–794（794 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 oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric	Chain s 1–794（794 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
9GY4 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map) Deposited 2024-10-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric	Chain E 1–794（794 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

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

View Construct and Data Evidence

UniProt name	UFL1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 16–809； UniProt 1–794

CDK5 regulatory subunit-associated protein 3

Homo sapiens

UniProt Q96JB5

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain C； UniProt 1–506	Not recorded	60S ribosomal protein L10a × 1 （P62906） E3 UFM1-protein ligase 1 × 1 （O94874） DDRGK domain-containing protein 1 × 1 （Q96HY6） Ubiquitin-fold modifier 1 × 1 （A0A8C2YGR4）	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 3.20 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8QFC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8OHD 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native) Deposited 2023-03-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain B 1–506（506 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain B 1–506（506 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric	Chain B 1–506（506 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
9GY4 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map) Deposited 2024-10-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric	Chain B 1–506（506 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

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

View Construct and Data Evidence

UniProt name	CK5P3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 6–511； UniProt 1–506

DDRGK domain-containing protein 1

Homo sapiens

UniProt Q96HY6

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain D； UniProt 29–314	Not recorded	60S ribosomal protein L10a × 1 （P62906） E3 UFM1-protein ligase 1 × 1 （O94874） CDK5 regulatory subunit-associated protein 3 × 1 （Q96JB5） Ubiquitin-fold modifier 1 × 1 （A0A8C2YGR4）	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 3.20 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8QFC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7W3N Crystal structure of Ufm1 fused to UFBP1 UFIM Deposited 2021-11-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 194–202（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；28% 2-propanol, 3% PEG 200, 0.1M MES at pH 6.0	Resolution 1.60 Å R-free 0.200
8B9X Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1 Deposited 2022-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 207–305（99 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Sodium acetate trihydrate Ammonium tartrate dibasic	Resolution 3.07 Å R-free 0.272
8B9X Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1 Deposited 2022-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 207–305（99 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Sodium acetate trihydrate Ammonium tartrate dibasic	Resolution 3.07 Å R-free 0.272
8C0D UFL1/DDRGK1 bound to UFC1 Deposited 2022-12-16	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 205–314（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；0.1M HEPES, 1.03M Li2SO4	Resolution 2.56 Å R-free 0.286
8C0D UFL1/DDRGK1 bound to UFC1 Deposited 2022-12-16	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 205–314（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；0.1M HEPES, 1.03M Li2SO4	Resolution 2.56 Å R-free 0.286
8OHD 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native) Deposited 2023-03-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain C 1–314（314 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8OJ0 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native) Deposited 2023-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain C 1–314（314 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8OJ5 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution) Deposited 2023-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric	Chain C 1–314（314 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
9GY4 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map) Deposited 2024-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric	Chain C 1–314（314 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

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

View Construct and Data Evidence

UniProt name	DDRGK_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 18–303； UniProt 29–314

Ubiquitin-fold modifier 1

Homo sapiens

UniProt A0A8C2YGR4

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain E； UniProt 112–198	Not recorded	60S ribosomal protein L10a × 1 （P62906） E3 UFM1-protein ligase 1 × 1 （O94874） CDK5 regulatory subunit-associated protein 3 × 1 （Q96JB5） DDRGK domain-containing protein 1 × 1 （Q96HY6）	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 3.20 Å

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A8C2YGR4_COTJA
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–87； UniProt 112–198

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8qfc
Deposition date deposition_date	2023-09-04
Structure title title	UFL1 E3 ligase bound 60S ribosome
Keywords keywords	UFM1, Ligase, Ribosome, Complex; LIGASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	78.20 Å
Radius of gyration Rg (electron density) rg_electron	78.67 Å
Forward intensity I(0) i0	331167000.00
Molecular weight molecular_weight	155560.0 kDa
Excluded volume excluded_volume	195850 Å³
Envelope volume envelope_volume	446760 Å³
Hydration-shell volume shell_volume	51187 Å³
Envelope diameter envelope_diameter	251.6 Å
Shell Rg shell_rg	69.03 Å
Envelope Rg envelope_rg	74.92 Å
Shape Rg shape_rg	78.71 Å
Total Rg total_rg	78.30 Å
Total atoms total_atoms	10968
Residues n_residues	1488
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	222.9 Å
Rg (real space) rg_real	78.51 Å
Rg uncertainty (real space) rg_real_error	1.79 Å
I(0) (real space) i0_real	3.3060e+08
I(0) uncertainty (real space) i0_real_error	6.6890e+06
Rg (reciprocal space) rg_reciprocal	75.40 Å
I(0) (reciprocal space) i0_reciprocal	328700000.0000
Solution quality estimate total_estimate	0.7030
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	33.4 Å
Skewness Skewness skewness	0.213
Kurtosis Kurtosis kurtosis	-1.075
Angular range angular_range	— – 0.1000 Å⁻¹
Current regularization parameter α current_alpha	0.0060
Highest regularization parameter α highest_alpha	10170000.0000
Real-space data points n_real_points	21
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.595; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.362; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	60S ribosomal protein L10a
Molecular weight formula_weight	24879.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10968

MSSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTHNENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQRLY

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	E3 UFM1-protein ligase 1
Molecular weight formula_weight	91591.2 kDa
EC 编号 ec_number	2.3.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGHHHHHHENLYFQGMADAWEEIRRLAADFQRAQFAEATQRLSERNCIEIVNKLIAQKQLEVVHTLDGKEYITPAQISKEMRDELHVRGGRVNIVDLQQVINVDLIHIENRIGDIIKSEKHVQLVLGQLIDENYLDRLAEEVNDKLQESGQVTISELCKTYDLPGNFLTQALTQRLGRIISGHIDLDNRGVIFTEAFVARHKARIRGLFSAITRPTAVNSLISKYGFQEQLLYSVLEELVNSGRLRGTVVGGRQDKAVFVPDIYSRTQSTWVDSFFRQNGYLEFDALSRLGIPDAVSYIKKRYKTTQLLFLKAACVGQGLVDQVEASVEEAISSGTWVDIAPLLPTSLSVEDAAILLQQVMRAFSKQASTVVFSDTVVVSEKFINDCTELFRELMHQKAEKEMKNNPVHLITEEDLKQISTLESVSTSKKDKKDERRRKATEGSGSMRGGGGGNAREYKIKKVKKKGRKDDDSDDESQSSHTGKKKPEISFMFQDEIEDFLRKHIQDAPEEFISELAEYLIKPLNKTYLEVVRSVFMSSTTSASGTGRKRTIKDLQEEVSNLYNNIRLFEKGMKFFADDTQAALTKHLLKSVCTDITNLIFNFLASDLMMAVDDPAAITSEIRKKILSKLSEETKVALTKLHNSLNEKSIEDFISCLDSAAEACDIMVKRGDKKRERQILFQHRQALAEQLKVTEDPALILHLTSVLLFQFSTHSMLHAPGRCVPQIIAFLNSKIPEDQHALLVKYQGLVVKQLVSQSKKTGQGDYPLNNELDKEQEDVASTTRKELQELSSSIKDLVLKSRKSSVTEE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	CDK5 regulatory subunit-associated protein 3
Molecular weight formula_weight	57458.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GPLVDMEDHQHVPIDIQTSKLLDWLVDRRHCSLKWQSLVLTIREKINAAIQDMPESEEIAQLLSGSYIHYFHCLRILDLLKGTEASTKNIFGRYSSQRMKDWQEIIALYEKDNTYLVELSSLLVRNVNYEIPSLKKQIAKCQQLQQEYSRKEEECQAGAAEMREQFYHSCKQYGITGENVRGELLALVKDLPSQLAEIGAAAQQSLGEAIDVYQASVGFVCESPTEQVLPMLRFVQKRGNSTVYEWRTGTEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEGTDSGISAEAAGIDWGIFPESDSKDPGGDGIDWGDDAVALQITVLEAGTQAPEGVARGPDALTLLEYTETRNQFLDELMELEIFLAQRAVELSEEADVLSVSQFQLAPAILQGQTKEKMVTMVSVLEDLIGKLTSLQLQHLFMILASPRYVDRVTEFLQQKLKQSQLLALKKELMVQKQQEALEEQAALEPKLDLLLEKTKELQKLIEADISKRYSGRPVNLMGTSL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	DDRGK domain-containing protein 1
Molecular weight formula_weight	34644.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MWSHPQFEKLEVLFQGPASAGQEPLHNEELAGAGRVAQPGPLEPEEPRAGGRPRRRRDLGSRLQAQRRAQRVAWAEADENEEEAVILAQEEEGVEKPAETHLSGKIGAKKLRKLEEKQARKAQREAEEAEREERKRLESQREAEWKKEEERLRLEEEQKEEEERKAREEQAQREHEEYLKLKEAFVVEEEGVGETMTEEQSQSFLTEFINYIKQSKVVLLEDLASQVGLRTQDTINRIQDLLAEGTITGVIDDRGKFIYITPEELAAVANFIRQRGRVSIAELAQASNSLIAWGRESPAQAPA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Ubiquitin-fold modifier 1
Molecular weight formula_weight	9236.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GPGSMSKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	299008

fit	/app/data/saxs_computation/qf/8qfc/8qfc.fit
pddf	/app/data/pr_computation/qf/8qfc/8qfc.pr.out
profile	/app/data/saxs_computation/qf/8qfc/8qfc.dat

UFL1 E3 ligase bound 60S ribosome

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

60S ribosomal protein L10a

State in the Current Structure

Other States of the Same Protein in the Database

E3 UFM1-protein ligase 1

State in the Current Structure

Other States of the Same Protein in the Database

CDK5 regulatory subunit-associated protein 3

State in the Current Structure

Other States of the Same Protein in the Database

DDRGK domain-containing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-fold modifier 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)