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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：J3QS39 New Search
39PDB entries
47Biological assembly
65chain/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
2DEN Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin Deposited 2006-02-14 Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 1mM HGB1-UBA | 20mM phosphate, 100mM NaCl, pH6.5
NMR sample composition 1mM Ubiquitin | 20mM phosphate, 100mM NaCl, pH6.5
Resolution not provided
2MBH NMR structure of EKLF(22-40)/Ubiquitin Complex Deposited 2013-07-31 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20
NMR sample composition 4 mM Ubi_unl, 0.8 mM [U-100% 15N] EKLF, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 4 mM EKLF_unl, 0.8 mM [U-100% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 4 mM EKLF_unl, 0.8 mM [U-100% 13C; U-100% 15N] Ubiquitin, 100% D2O | 100% D2O
NMR sample composition 4 mM Ubi_unl, 0.8 mM [U-100% 13C; U-100% 15N] EKLF, 100% D2O | 100% D2O
Resolution not provided
3PRM Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin Deposited 2010-11-30 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；22-26% PEG 8000, 0.1 M Na cacodylate, 0.2 M Mg acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.267
3PRM Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin Deposited 2010-11-30 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain D 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；22-26% PEG 8000, 0.1 M Na cacodylate, 0.2 M Mg acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.267
3PRP Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin Deposited 2010-11-30 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；22-28% PEG 8000, 100 mM Na cacodylate pH 6.5, 100-250 mM Mg acetate, and 2% n-Octyl- -D-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.212
3PRP Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin Deposited 2010-11-30 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain D 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；22-28% PEG 8000, 100 mM Na cacodylate pH 6.5, 100-250 mM Mg acetate, and 2% n-Octyl- -D-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.212
5TXK CRYSTAL STRUCTURE OF USP35 C450S IN COMPLEX WITH UBIQUITIN Deposited 2016-11-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 1–76（76 aa）
Not recorded SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；296 K；0.95 M ammonium sulphate 0.1 M HEPES
Resolution 1.84 Å R-free 0.183
5YDR Structure of DNMT1 RFTS domain in complex with ubiquitin Deposited 2017-09-14 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain A 1–73（73 aa） Fragment：UNP residues 1-73
Chain D 1–73（73 aa） Fragment：UNP residues 1-73
Not recorded PO4 PHOSPHATE ION × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；291 K；20mM Tris-HCl, 200mM sodium acetate, 25% PEG 4000
Resolution 2.00 Å R-free 0.233
6K4I The partially disordered conformation of ubiquitin (Q41N variant) Deposited 2019-05-24 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–76（76 aa）
Mutation：Q41N No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4；278 K；Ionic strength (raw mmCIF value) 30；Pressure 2500
NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] ubiquitin, 30 mM D D-acetate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.3 mM [U-99% 15N] ubiquitin, 30 mM D D-acetate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6KOW Retracted state of S65/T66 double-phosphorylated ubiquitin Deposited 2019-08-13 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 20 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6KOX Relaxed state of S65/T66 double-phosphorylated ubiquitin Deposited 2019-08-13 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 20 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6NJG Ubiquitin Variant in Complex with Ubiquitin Interacting Motif Deposited 2019-01-03 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain C 1–78（78 aa）
Mutation：K6Q, L8I, G10V, K11M, T12R, T14A, K48M, Q62K, K63R, E64D, T66N, H68Y, L71S, R72S, G75S, G76L, M77R, Q78A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.1 M DL-Malic acid
Resolution 2.35 Å R-free 0.244
6NOG Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome Deposited 2019-01-16 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain L 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing
Resolution 3.90 Å
6O96 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Deposited 2019-03-13 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain L 1–76（76 aa）
Mutation：G76C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen PROPANE；blotted for 3s before plunging
Resolution 3.50 Å
6OAM Crystal Structure of ChlaDUB2 DUB domain Deposited 2019-03-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain D 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES sodium pH 7.5, 0.8 M sodium phosphate monobasic monohydrate, 0.8 M sodium phosphate monobasic, 0.1M Cesium chloride
Resolution 2.50 Å R-free 0.306
6OAM Crystal Structure of ChlaDUB2 DUB domain Deposited 2019-03-17 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES sodium pH 7.5, 0.8 M sodium phosphate monobasic monohydrate, 0.8 M sodium phosphate monobasic, 0.1M Cesium chloride
Resolution 2.50 Å R-free 0.306
6PZV Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Deposited 2019-08-01 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded FLC CITRATE ANION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；277 K；0.1M citric acid (pH 3.5), 28% PEG8000
Resolution 3.01 Å R-free 0.272
6PZV Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Deposited 2019-08-01 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；277 K；0.1M citric acid (pH 3.5), 28% PEG8000
Resolution 3.01 Å R-free 0.272
6QF8 Solution NMR ensemble for human ubiquitin at 298K compiled using the CoMAND method Deposited 2019-01-09 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] human ubiquitin, 40 mM sodium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6TBM Structure of SAGA bound to TBP, including Spt8 and DUB Deposited 2019-11-01 Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric（18） Consistent with protein count
Chain R 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
6UH5 Structural basis of COMPASS eCM recognition of the H2Bub nucleosome Deposited 2019-09-26 Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric（19） Consistent with all polymers
Chain Q 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6XAA SARS CoV-2 PLpro in complex with ubiquitin propargylamide Deposited 2020-06-04 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 1–76（76 aa）
Mutation：G76 replaced with propargylamide Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.2 M sodium acetate, 0.1 M Tris chloride, pH 8.5
Resolution 2.70 Å R-free 0.260
6XQC UbKEKS Deposited 2020-07-09 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 500 uM [U-13C; U-15N] UbKEKS, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 500 uM [U-13C; U-15N] UbKEKS, 100% D2O | 100% D2O
Resolution not provided
7BBD Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2 Deposited 2020-12-17 Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain B 1–74（74 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290.15 K；MOPSO, Bis-Tris, PEG 4K, 1,2,6-hexanetriol, Li, Na, K
Resolution 2.20 Å R-free 0.252
7BU0 Crystal structure of a OTU deubiquitinase in complex with Ub-PA Deposited 2020-04-03 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain C 1–75（75 aa）
Chain D 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289.15 K；0.1M Magnesium formate dihydrate 15% w/v PEG 3350
Resolution 2.43 Å R-free 0.255
7E8I Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Deposited 2021-03-01 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain L 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7NBB Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3 Deposited 2021-01-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 1–72（72 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R MG MAGNESIUM ION × 4 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277.15 K；0.1 M Bis-Tris pH 7.2 0.28 M MgCl2 21% PEG3350 0.15 M NaCl 0.05 M Tris/HCl pH 7.5
Resolution 1.55 Å R-free 0.212
7NBB Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3 Deposited 2021-01-26 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain E 1–72（72 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R MG MAGNESIUM ION × 3 GOL GLYCEROL × 1 CL CHLORIDE ION × 5 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277.15 K；0.1 M Bis-Tris pH 7.2 0.28 M MgCl2 21% PEG3350 0.15 M NaCl 0.05 M Tris/HCl pH 7.5
Resolution 1.55 Å R-free 0.212
7NPO Branched K48-K63-Ub3 Deposited 2021-02-27 Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain A 1–72（72 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium acetate, 20 mM Tris pH 7.5, 50 mM NaCl, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v PEG 4000; 22 mg/ml
Resolution 2.19 Å R-free 0.284
7QO4 26S proteasome WT-Ubp6-UbVS complex in the si state (ATPases, Rpn1, Ubp6, and UbVS) Deposited 2021-12-23 Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count
Chain 9 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
7QO6 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state Deposited 2021-12-23 Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric（49） Consistent with protein count
Chain 9 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric（17） Consistent with all polymers
Chain O 1–76（76 aa）
Mutation：G76C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7US1 Structure of parkin (R0RB) bound to two phospho-ubiquitin molecules Deposited 2022-04-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 1–74（74 aa）
Chain C 1–74（74 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；0.1M Bis-Tris propane pH 7.5, 20.5% PEG3350, 0.2M NaI
Resolution 2.48 Å R-free 0.258
7W3U USP34 catalytic domain in complex with UbPA Deposited 2021-11-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% w/v PEG 3350, 0.8M Magnesium chloride hexahydrate, 0.6mM Lyso PG, 1 mM Facade R-EPC
Resolution 3.13 Å R-free 0.245
7W3U USP34 catalytic domain in complex with UbPA Deposited 2021-11-26 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain E 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% w/v PEG 3350, 0.8M Magnesium chloride hexahydrate, 0.6mM Lyso PG, 1 mM Facade R-EPC
Resolution 3.13 Å R-free 0.245
7W3U USP34 catalytic domain in complex with UbPA Deposited 2021-11-26 Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% w/v PEG 3350, 0.8M Magnesium chloride hexahydrate, 0.6mM Lyso PG, 1 mM Facade R-EPC
Resolution 3.13 Å R-free 0.245
7W54 Crystal structure of a bacterial OTU DUB with Ub-PA Deposited 2021-11-29 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain C 1–75（75 aa）
Chain D 1–75（75 aa）
Chain E 1–75（75 aa）
Chain F 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；299 K；100 mM Magnesium formate, 15% (w/v) PEG 3350, pH 8.0
Resolution 2.64 Å R-free 0.253
7YQK cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 Deposited 2022-08-07 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain O 1–75（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
8A67 Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with matured synthetic nanobody NbSL3.3Q (3rd generation) Deposited 2022-06-16 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 1–72（72 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；Protein concentrated to 14.5 mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl. Mixed 200 nl protein with 100 nl mother liquor (0.1 M HEPES pH 7.5, 10% 2-propanol, 20% PEG4000). Crystals harvested and cryo-protected with Mother liquor supplemented with 30% glycerol.
Resolution 1.86 Å R-free 0.245
8A67 Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with matured synthetic nanobody NbSL3.3Q (3rd generation) Deposited 2022-06-16 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain E 1–72（72 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；Protein concentrated to 14.5 mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl. Mixed 200 nl protein with 100 nl mother liquor (0.1 M HEPES pH 7.5, 10% 2-propanol, 20% PEG4000). Crystals harvested and cryo-protected with Mother liquor supplemented with 30% glycerol.
Resolution 1.86 Å R-free 0.245
8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain O 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8HQY Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom Deposited 2022-12-14 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain U 1–74（74 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8K6E LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 1–75（75 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；PEG 8000; Sodium chloride; Sodium HEPES
Resolution 2.74 Å R-free 0.245
8T2D Ubiquitin variant i53:Mutant T12Y.T14E.L67R with 53BP1 Tudor domain Deposited 2023-06-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 1–74（74 aa）
Mutation：T12Y, T14E, L67R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.1 M MES pH 6.0, 0.2 M Trimethylamine N-oxide dehydrate, 13% w/v PEG MME 2000
Resolution 1.75 Å R-free 0.273
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain U 1–75（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9NY4 USP21 bound to H2AK119ub nucleosome Deposited 2025-03-26 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers
Chain U 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 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.