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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：Q99496 New Search
25PDB entries
37Biological assembly
44chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
2H0D Structure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex Deposited 2006-05-14 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 15–114（100 aa） Fragment：residues 15-114
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；20 mM Tris, 500 mM NaCl, 1 mM EDTA, 1.5 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.50 Å R-free 0.244
3GS2 Ring1B C-terminal domain/Cbx7 Cbox Complex Deposited 2009-03-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 223–333（111 aa） Fragment：C-terminal domain, residues 223-333
Chain C 223–333（111 aa） Fragment：C-terminal domain, residues 223-333
Mutation：N306D Mutation：N306D SO4 SULFATE ION × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；25% PEG MME 550, 0.1 M MES, 0.01 M zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.70 Å R-free 0.243
3GS2 Ring1B C-terminal domain/Cbx7 Cbox Complex Deposited 2009-03-26 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 223–333（111 aa） Fragment：C-terminal domain, residues 223-333
Mutation：N306D SO4 SULFATE ION × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；25% PEG MME 550, 0.1 M MES, 0.01 M zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.70 Å R-free 0.243
3GS2 Ring1B C-terminal domain/Cbx7 Cbox Complex Deposited 2009-03-26 Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 223–333（111 aa） Fragment：C-terminal domain, residues 223-333
Mutation：N306D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；25% PEG MME 550, 0.1 M MES, 0.01 M zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.70 Å R-free 0.243
3H8H Structure of the C-terminal domain of human RNF2/RING1B; Deposited 2009-04-29 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 220–330（111 aa） Fragment：RESIDUES 220-330
Not recorded 2PE NONAETHYLENE GLYCOL × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；289 K；2 M AMMONIUM SULPHATE, 2% PEG 400, 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K
Resolution 2.00 Å R-free 0.244
3H8H Structure of the C-terminal domain of human RNF2/RING1B; Deposited 2009-04-29 Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 220–330（111 aa） Fragment：RESIDUES 220-330
Not recorded 2PE NONAETHYLENE GLYCOL × 2 GOL GLYCEROL × 2 SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；289 K；2 M AMMONIUM SULPHATE, 2% PEG 400, 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K
Resolution 2.00 Å R-free 0.244
3H8H Structure of the C-terminal domain of human RNF2/RING1B; Deposited 2009-04-29 Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 220–330（111 aa） Fragment：RESIDUES 220-330
Not recorded 2PE NONAETHYLENE GLYCOL × 2 GOL GLYCEROL × 2 SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；289 K；2 M AMMONIUM SULPHATE, 2% PEG 400, 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K
Resolution 2.00 Å R-free 0.244
3H8H Structure of the C-terminal domain of human RNF2/RING1B; Deposited 2009-04-29 Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 220–330（111 aa） Fragment：RESIDUES 220-330
Not recorded 2PE NONAETHYLENE GLYCOL × 2 GOL GLYCEROL × 2 SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；289 K；2 M AMMONIUM SULPHATE, 2% PEG 400, 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K
Resolution 2.00 Å R-free 0.244
3IXS Ring1B C-terminal domain/RYBP C-terminal domain Complex Deposited 2009-09-04 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 223–333（111 aa） Fragment：C-terminal Domain (UNP residues 223-333)
Mutation：N306D EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；32% PEG 1750, 0.125 M lithium sulfate, 10% ethylene glycol, 50 mM CHES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.70 Å R-free 0.234
3IXS Ring1B C-terminal domain/RYBP C-terminal domain Complex Deposited 2009-09-04 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 223–333（111 aa） Fragment：C-terminal Domain (UNP residues 223-333)
Mutation：N306D EDO 1,2-ETHANEDIOL × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；32% PEG 1750, 0.125 M lithium sulfate, 10% ethylene glycol, 50 mM CHES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.70 Å R-free 0.234
3IXS Ring1B C-terminal domain/RYBP C-terminal domain Complex Deposited 2009-09-04 Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain E 223–333（111 aa） Fragment：C-terminal Domain (UNP residues 223-333)
Mutation：N306D EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；32% PEG 1750, 0.125 M lithium sulfate, 10% ethylene glycol, 50 mM CHES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.70 Å R-free 0.234
3IXS Ring1B C-terminal domain/RYBP C-terminal domain Complex Deposited 2009-09-04 Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain G 223–333（111 aa） Fragment：C-terminal Domain (UNP residues 223-333)
Mutation：N306D EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；32% PEG 1750, 0.125 M lithium sulfate, 10% ethylene glycol, 50 mM CHES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.70 Å R-free 0.234
3IXS Ring1B C-terminal domain/RYBP C-terminal domain Complex Deposited 2009-09-04 Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain I 223–333（111 aa） Fragment：C-terminal Domain (UNP residues 223-333)
Mutation：N306D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；32% PEG 1750, 0.125 M lithium sulfate, 10% ethylene glycol, 50 mM CHES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.70 Å R-free 0.234
3IXS Ring1B C-terminal domain/RYBP C-terminal domain Complex Deposited 2009-09-04 Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain K 223–333（111 aa） Fragment：C-terminal Domain (UNP residues 223-333)
Mutation：N306D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；32% PEG 1750, 0.125 M lithium sulfate, 10% ethylene glycol, 50 mM CHES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.70 Å R-free 0.234
3RPG Bmi1/Ring1b-UbcH5c complex structure Deposited 2011-04-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 1–116（116 aa） Fragment：UNP Residues 1-116
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；40% MPD, 0.1 M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.65 Å R-free 0.243
3RPG Bmi1/Ring1b-UbcH5c complex structure Deposited 2011-04-26 Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 1–116（116 aa） Fragment：UNP Residues 1-116
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；40% MPD, 0.1 M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.65 Å R-free 0.243
4R8P Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle Deposited 2014-09-02 Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain L 2–116（115 aa） Fragment：Residues 2-116 of Ring1B and Residues 2-148 of UbcH5c
Chain N 2–116（115 aa） Fragment：Residues 2-116 of Ring1B and Residues 2-148 of UbcH5c
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions Modified micro batch under oil；pH 7.5；294 K；25 mM HEPES pH 7.5, 80 mM NH4NO3, 3 % PEG2000-MME, Modified micro batch under oil, temperature 294K
Resolution 3.28 Å R-free 0.245
4S3O PCGF5-RING1B-UbcH5c complex Deposited 2015-03-23 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain E 1–116（116 aa） Fragment：RING domain, UNP residues 1-116
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；13.5% PEG 550 MME, 10 mM TCEP, 0.1 M MES pH 6.5, 100 mM KCl, VAPOR DIFFUSION, temperature 277K
Resolution 2.00 Å R-free 0.237
4S3O PCGF5-RING1B-UbcH5c complex Deposited 2015-03-23 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 1–116（116 aa） Fragment：RING domain, UNP residues 1-116
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；13.5% PEG 550 MME, 10 mM TCEP, 0.1 M MES pH 6.5, 100 mM KCl, VAPOR DIFFUSION, temperature 277K
Resolution 2.00 Å R-free 0.237
7ND1 First-in-class small molecule inhibitors of Polycomb Repressive Complex 1 (PRC1) RING domain Deposited 2021-01-29 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 10–116（107 aa）
Not recorded ZN ZINC ION × 4 U9E 3-(2-chlorophenyl)-4-ethyl-5-(1~{H}-indol-4-yl)-1~{H}-pyrrole-2-carboxylic acid × 1 SOLUTION NMR
NMR measurement conditions pH 6.8；303.3 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 0.12 mM [U-2H; U-13C; U-15N; CH3 ILV] Ring1B-BMI1, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
8GRM Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Deposited 2022-09-02 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain N 16–116（101 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8PP7 human RYBP-PRC1 bound to mononucleosome Deposited 2023-07-06 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers
Chain L 1–336（336 aa）
Chain N 1–336（336 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
9DBY ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Deposited 2024-08-24 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers
Chain L 1–336（336 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9DDE ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Deposited 2024-08-28 Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric（15） Consistent with all polymers
Chain L 1–336（336 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9DGG ncPRC1RYBP bound to unmodified nucleosome Deposited 2024-09-02 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers
Chain L 1–336（336 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9V6Q Cryo-EM structure of two cPRC1 complexes bound to opposite faces of an endogenous 147-bp mono-nucleosome Deposited 2025-05-27 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain L 1–336（336 aa）
Chain N 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.60 Å
9V6S Cryo-EM structure of a single cPRC1 complex engaged on one face of an endogenous 147-bp mononucleosome Deposited 2025-05-27 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain N 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9V6X Cryo-EM structure of the cPRC1 complex bound to an endogenous 184-bp mono-nucleosome Deposited 2025-05-27 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain N 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.00 Å
9V8L Cryo-EM structure of the cPRC1-di-nucleosome (loose) complex Deposited 2025-05-29 Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers
Chain N 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 6.60 Å
9V9H Cryo-EM structure of the cPRC1-di-nucleosome (tight) complex Deposited 2025-05-30 Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers
Chain T 1–336（336 aa）
Chain V 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.50 Å
9V9P Cryo-EM structure of the cPRC1-di-nucleosome (CBX7) complex Deposited 2025-06-01 Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric（24） Consistent with all polymers
Chain U 1–336（336 aa）
Chain W 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.40 Å
9V9Q Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain N 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.80 Å
9V9R Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain N 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
9V9U Cryo-EM structure of the ncPRC1.4 complex containing two RNF2-BMI1 bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric（16） Consistent with all polymers
Chain L 1–336（336 aa）
Chain N 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.70 Å
9V9V Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain N 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.80 Å
9V9X Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain N 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.30 Å
9V9Y Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain N 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.