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6fdk

Structure of Chlamydia trachomatis effector protein Cdu1 bound to ubiquitin

Method: X-RAY DIFFRACTION Dmax: 67.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Deubiquitinase and deneddylase Dub1

Chlamydia trachomatis 434/Bu

UniProt B0B9A0

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 155–401 Mutation：C174A, C226S, C386A Polyubiquitin-B × 1 （P0CG47） CL CHLORIDE ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M MES pH 6.5, 12% PEG 20000 Resolution 1.60 Å R-free 0.203

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 6FDK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5HAG Structure of Chlamydia trachomatis effector protein ChlaDUB1 Deposited 2015-12-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 130–401（272 aa） Fragment：UNP residues 130-401
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES (pH 7.5), 20% PEG 8000
Resolution 2.10 Å R-free 0.208
6FDQ Structure of Chlamydia trachomatis effector protein Cdu1 bound to Compound 5 Deposited 2017-12-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 155–401（247 aa）
Not recorded 2UQ N-benzyl-2-[(Z)-iminomethyl]pyrimidine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；100 mM Bicine pH 9.0, 10% PEG 20000, 2% 1, 4 dioxane
Resolution 2.30 Å R-free 0.284
6FDQ Structure of Chlamydia trachomatis effector protein Cdu1 bound to Compound 5 Deposited 2017-12-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 155–401（247 aa）
Not recorded 2UQ N-benzyl-2-[(Z)-iminomethyl]pyrimidine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；100 mM Bicine pH 9.0, 10% PEG 20000, 2% 1, 4 dioxane
Resolution 2.30 Å R-free 0.284
6FDU Structure of Chlamydia trachomatis effector protein Cdu1 bound to Compound 3 Deposited 2017-12-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 155–401（247 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；100 mM Bicine pH 9.0, 10% PEG 20000, 2% 1, 4 dioxane
Resolution 2.30 Å R-free 0.240
6FDU Structure of Chlamydia trachomatis effector protein Cdu1 bound to Compound 3 Deposited 2017-12-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 155–401（247 aa）
Not recorded CL CHLORIDE ION × 1 D5W (2~{S},3~{S})-2-[[(2~{S})-2-[3,5-bis(chloranyl)phenyl]-2-(dimethylamino)ethanoyl]amino]-~{N}-[[2-(iminomethyl)pyrimidin-4-yl]methyl]-3-methyl-pentanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；100 mM Bicine pH 9.0, 10% PEG 20000, 2% 1, 4 dioxane
Resolution 2.30 Å R-free 0.240
6GZS Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to ubiquitin Deposited 2018-07-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 130–401（272 aa）
Not recorded GOL GLYCEROL × 1 SO4 SULFATE ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MES (pH 6.0), 20% PEG 6000
Resolution 1.90 Å R-free 0.213
6GZT Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to Coenzyme A Deposited 2018-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 130–401（272 aa） Fragment：UNP residues 130-401
Not recorded GOL GLYCEROL × 4 SO4 SULFATE ION × 1 COA COENZYME A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES (pH 7.2), 20% PEG 8000
Resolution 2.10 Å R-free 0.216

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

View Construct and Data Evidence
UniProt name CDUB1_CHLT2
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 20–266； UniProt 155–401

Polyubiquitin-B

Homo sapiens

UniProt P0CG47

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–75 Not recorded Deubiquitinase and deneddylase Dub1 × 1 （B0B9A0） CL CHLORIDE ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M MES pH 6.5, 12% PEG 20000 Resolution 1.60 Å R-free 0.203

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 6FDK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2MBB Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex Deposited 2013-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：UNP P0CG47 residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 3 mM [U-100% 15N] GB1-UBM1, 3 mM [U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 3 mM GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
Resolution not provided
2MRO Structure of the complex of ubiquitin and the UBA domain from DNA-damage-inducible 1 protein (Ddi1) Deposited 2014-07-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：Human Ubiquitin
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298.2 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 1 mM [U-100% 15N] Ub-1, 20 mM sodium phosphate-2, 7 % [U-99% 2H] D2O-3, 93 % H2O-4, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 1 mM [U-100% 15N] UBA-5, 20 mM sodium phosphate-6, 7 % [U-99% 2H] D2O-7, 93 % H2O-8, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
2MSG Solid-state NMR structure of ubiquitin Deposited 2014-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–78（72 aa） Fragment：UNP residuse 1-72
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions 273 K；Pressure ambient
NMR sample composition 20 mg [U-100% 13C; U-100% 15N] Ubiquitin, 30 mg [1-glucose 13C,U-100% 15N] Ubiquitin, 40 mg [2-glucose 13C,U-100% 15N] Ubiquitin, 40 % v/v MPD, 0.2 M CdCl2, 1 mg DSS, 100% H20 | 100% H20
Resolution not provided
2N13 Complex structure of MyUb (1080-1122) of human Myosin VI with K63-diUb Deposited 2015-03-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；283 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.5 mM [U-13C; U-15N] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2Y5B Structure of USP21 in complex with linear diubiquitin-aldehyde Deposited 2011-01-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–152（152 aa） Fragment：LINEAR DIUBIQUITIN ALDEHYDE, RESIDUES 1-152
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；15% PEG8000, 0.2 M NH4SO4, pH 7.4
Resolution 2.70 Å R-free 0.279
2Y5B Structure of USP21 in complex with linear diubiquitin-aldehyde Deposited 2011-01-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–152（152 aa） Fragment：LINEAR DIUBIQUITIN ALDEHYDE, RESIDUES 1-152
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；15% PEG8000, 0.2 M NH4SO4, pH 7.4
Resolution 2.70 Å R-free 0.279
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Chain H 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Chain C 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Chain D 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ4 Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.1；292 K；0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K
Resolution 3.40 Å R-free 0.319
3OJ4 Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.1；292 K；0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K
Resolution 3.40 Å R-free 0.319
3ONS Crystal structure of Human Ubiquitin in a new crystal form Deposited 2010-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–72（72 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；277 K；2 ul of a 10 mg/ml protein solution was mixed with 2 ul of the reservoir solution (50-56 % MPD and 8-18 % (v/v) glycerol solution in 27mM sodium citrate (pH 4.0-4.2) buffer), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.211
3PTF X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin Deposited 2010-12-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：Ubiquitin
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.70 Å R-free 0.275
3PTF X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin Deposited 2010-12-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：Ubiquitin
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.70 Å R-free 0.275
3ZLZ Lys6-linked tri-ubiquitin Deposited 2013-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：YES Mutation：YES ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4
Resolution 2.90 Å R-free 0.288
3ZLZ Lys6-linked tri-ubiquitin Deposited 2013-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Mutation：YES ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4
Resolution 2.90 Å R-free 0.288
3ZLZ Lys6-linked tri-ubiquitin Deposited 2013-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Mutation：YES ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4
Resolution 2.90 Å R-free 0.288
3ZNH Crimean Congo Hemorrhagic Fever Virus OTU domain in complex with ubiquitin-propargyl. Deposited 2013-02-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；20-30% PEG 8000, 100 MM NA CACODYLATE PH 6.5, 100 MM MG ACETATE, AND 2% N-OCTYL-BETA-D-GLUCOSIDE.
Resolution 2.30 Å R-free 0.275
4UEL UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain Deposited 2014-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM BIS-TRIS-PROPANE PH 5.8, 300 MM NABR, 21% PEG3350. 4 DEGREES CELSIUS
Resolution 2.30 Å R-free 0.234
4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
Resolution 3.69 Å R-free 0.269
4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
Resolution 3.69 Å R-free 0.269
4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
Resolution 3.69 Å R-free 0.269
4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
Resolution 3.69 Å R-free 0.269
4WHV E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B Deposited 2014-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–76（76 aa） Fragment：unp residues 1-76
Chain F 1–76（76 aa） Fragment：unp residues 1-76
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；1.04 M (NH4)2HPO4
Resolution 8.30 Å R-free 0.337
4WHV E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B Deposited 2014-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 1–76（76 aa） Fragment：unp residues 1-76
Chain L 1–76（76 aa） Fragment：unp residues 1-76
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；1.04 M (NH4)2HPO4
Resolution 8.30 Å R-free 0.337
4WLR Crystal Structure of mUCH37-hRPN13 CTD-hUb complex Deposited 2014-10-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；277 K；25% PEG 3350, 220 mM MgCl2,100 mM Bis-Tris
Resolution 2.00 Å R-free 0.227
4WUR The crystal structure of the MERS-CoV papain-like protease (C111S) with human ubiquitin Deposited 2014-11-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded IPA ISOPROPYL ALCOHOL × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；291 K；22% w/v PEG 4000, 15% v/v 2-propanol, 0.1M tri-sodium citrate pH 4.8 and 10% glycerol
Resolution 3.16 Å R-free 0.252
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
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, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
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, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
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, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4XOF Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin crystals without Zinc. Deposited 2015-01-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0
Resolution 1.15 Å R-free 0.171
4ZFR Catalytic domain of Sst2 F403A mutant bound to ubiquitin Deposited 2015-04-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–152（76 aa） Fragment：unp residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2M sodium citrate tribasic diehydrate, 0.1M HEPES sodium, 20% v/v 2-propanol
Resolution 1.72 Å R-free 0.237
4ZFT Catalytic domain of Sst2 F403W mutant bound to ubiquitin Deposited 2015-04-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–152（76 aa） Fragment：unp residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；(0.04 M Citric acid, 0.06 M BIS-TRIS propane), 20% w/v PEG 3,350
Resolution 2.30 Å R-free 0.235
4ZFT Catalytic domain of Sst2 F403W mutant bound to ubiquitin Deposited 2015-04-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 77–152（76 aa） Fragment：unp residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；(0.04 M Citric acid, 0.06 M BIS-TRIS propane), 20% w/v PEG 3,350
Resolution 2.30 Å R-free 0.235
4ZPZ Crystal Structure of Semi-synthetic Ubiquitin with Phospho-Ser65 and Ala46Cys Deposited 2015-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–73（73 aa） Fragment：ubiquitin, UNP residues 1-73
Chain B 1–73（73 aa） Fragment：ubiquitin, UNP residues 1-73
Mutation：A46C, Phospho-Ser65 Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：A46C, Phospho-Ser65 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 5；291 K；50 mM sodium cacodylate, 25% PEG 4000
Resolution 1.54 Å R-free 0.173
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain X 1–76（76 aa）
Chain c 1–76（76 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain h 1–76（76 aa）
Chain m 1–76（76 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
Resolution 2.49 Å R-free 0.304
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
Resolution 2.49 Å R-free 0.304
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
Resolution 2.49 Å R-free 0.304
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
Resolution 2.49 Å R-free 0.304
5CAW Structure of Pediculus humanus Parkin bound to phospho-ubiquitin Deposited 2015-06-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76 exchanged to chemical probe Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2% (v/v) PEG400, 2 M NH4SO4, 0.1 M HEPES pH 7.5
Resolution 2.62 Å R-free 0.260
5CAW Structure of Pediculus humanus Parkin bound to phospho-ubiquitin Deposited 2015-06-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Mutation：G76 exchanged to chemical probe Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2% (v/v) PEG400, 2 M NH4SO4, 0.1 M HEPES pH 7.5
Resolution 2.62 Å R-free 0.260
5CRA Structure of the SdeA DUB Domain Deposited 2015-07-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa） Fragment：UNP residues 1-75
Not recorded SO4 SULFATE ION × 6 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris:HCl, 3.0 M Sodium Chloride
Resolution 2.64 Å R-free 0.236
5CRA Structure of the SdeA DUB Domain Deposited 2015-07-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa） Fragment：UNP residues 1-75
Not recorded SO4 SULFATE ION × 3 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris:HCl, 3.0 M Sodium Chloride
Resolution 2.64 Å R-free 0.236
5CVM USP46~ubiquitin BEA covalent complex Deposited 2015-07-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–59（59 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；3.6 M sodium formate
Resolution 1.90 Å R-free 0.197
5CVN WDR48 (2-580):USP46~ubiquitin ternary complex Deposited 2015-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；292 K；0.1 M sodium chloride, 5% ethanol, 15% MPD, 0.1 M Tris pH 8.8
Resolution 3.36 Å R-free 0.222
5CVO WDR48:USP46~ubiquitin ternary complex Deposited 2015-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；15% MPD, 0.1 M NaCl, 0.1 M HEPES, pH 7.0
Resolution 3.88 Å R-free 0.275
5CVO WDR48:USP46~ubiquitin ternary complex Deposited 2015-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；15% MPD, 0.1 M NaCl, 0.1 M HEPES, pH 7.0
Resolution 3.88 Å R-free 0.275
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0M Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded PO4 PHOSPHATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；SPG buffer, PEG 1500
Resolution 1.91 Å R-free 0.213
5DFL Crystal structure of Ube2K~Ubiquitin conjugate Deposited 2015-08-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M di-ammonium citrate pH 5.0, 20% PEG 3350
Resolution 2.10 Å R-free 0.235
5DK8 Human ubiquitin in the P1 space group Deposited 2015-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–75（74 aa） Fragment：Ubiquitin, UNP residues 2-75
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；288 K；0.2M magnesium chloride hexahydrate, 30% w/v PEG 4000, 0.1 M Tris pH 8.5
Resolution 1.32 Å R-free 0.201
5DK8 Human ubiquitin in the P1 space group Deposited 2015-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–75（74 aa） Fragment：Ubiquitin, UNP residues 2-75
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；288 K；0.2M magnesium chloride hexahydrate, 30% w/v PEG 4000, 0.1 M Tris pH 8.5
Resolution 1.32 Å R-free 0.201
5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded ACT ACETATE ION × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
Resolution 2.85 Å R-free 0.264
5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–75（75 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
Resolution 2.85 Å R-free 0.264
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
Chain G 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Chain G 1–76（76 aa） Fragment：UNP residues 1-76
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EMZ Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit Deposited 2015-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：F45W SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；LiSO Tris PEG-3350
Resolution 1.66 Å R-free 0.209
5EMZ Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit Deposited 2015-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Mutation：F45W SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；LiSO Tris PEG-3350
Resolution 1.66 Å R-free 0.209
5EMZ Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit Deposited 2015-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Mutation：F45W SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；LiSO Tris PEG-3350
Resolution 1.66 Å R-free 0.209
5EYA TRIM25 RING domain in complex with Ubc13-Ub conjugate Deposited 2015-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Li citrate, 20% PEG 3350
Resolution 2.40 Å R-free 0.228
5GJQ Structure of the human 26S proteasome bound to USP14-UbAl Deposited 2016-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2 seconds before plunging
Resolution 4.35 Å
5GO7 Linear tri-ubiquitin Deposited 2016-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；0.2M sodium dihydrogen phosphate, 20% PEG 3350, PH 6.0
Resolution 1.80 Å R-free 0.310
5GO8 Linear tetra-ubiquitin Deposited 2016-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；0.2M Sodium acetate trihydrate, 20% PEG 3350, PH8.0
Resolution 2.21 Å R-free 0.322
5GOB Lys6-linked di-ubiquitin Deposited 2016-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；289 K；0.2M Magnesium chloride hexahydrate, 20% PEG 3350, PH5.9
Resolution 1.15 Å R-free 0.229
5GOC Lys11-linked diubiquitin Deposited 2016-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Li2SO4, 0.1M tris 8.5, 30% PEG 4000
Resolution 1.73 Å R-free 0.235
5GOD Lys27-linked di-ubiquitin Deposited 2016-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium acetate tetrahydrate, 0.1M Sodium cacodylate trihydrate PH6.5, 20% PEG 8000
Resolution 1.15 Å R-free 0.222
5GOG Lys29-linked di-ubiquitin Deposited 2016-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Potassium sulfate, 20% PEG 3350
Resolution 1.98 Å R-free 0.330
5GOH Lys33-linked di-ubiquitin Deposited 2016-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium sulfate heptahydrate, 20% peg 3350
Resolution 1.95 Å R-free 0.271
5GOI Lys48-linked di-ubiquitin Deposited 2016-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1M Sodium citrate tribasic dehydrate PH5.6, 20% 2-Propanol, 20%PEG 4000
Resolution 1.59 Å R-free 0.311
5GOJ Lys63-linked di-ubiquitin Deposited 2016-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1M TRIS hydrochloride PH8.5, 2.0M Ammonium phosphate monobasic
Resolution 1.55 Å R-free 0.253
5GOK K11/K63-branched tri-Ubiquitin Deposited 2016-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；0.2M MgSO4, 20% PEG 3350, 4mM CdCl2, PH6.0
Resolution 1.84 Å R-free 0.245
5H7S Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain Deposited 2016-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；0.04 M Citric acid, 0.06 M BIS-TRIS propane, pH 6.4, 20% w/v polyethylene glycol 3350
Resolution 3.49 Å R-free 0.286
5IBK Skp1-F-box in complex with a ubiquitin variant Deposited 2016-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 75–150（76 aa） Fragment：UNP residues 75-150
Mutation：L8G, T9A, G10R, K11T, T12A, R42I, A46S, G47R, Q49L, Q62H, K63R, H68R, R72I, L73F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol
Resolution 2.50 Å R-free 0.240
5IBK Skp1-F-box in complex with a ubiquitin variant Deposited 2016-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 75–150（76 aa） Fragment：UNP residues 75-150
Mutation：L8G, T9A, G10R, K11T, T12A, R42I, A46S, G47R, Q49L, Q62H, K63R, H68R, R72I, L73F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol
Resolution 2.50 Å R-free 0.240
5IFR Structure of the stable UBE2D3-UbDha conjugate Deposited 2016-02-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；200mM tripotassium citrate, 20% PEG 3350
Resolution 2.20 Å R-free 0.243
5J8P Lys27-linked diubiquitin Deposited 2016-04-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.2M magnesium acetate tetrahydrate, 0.1M sodium cacodylate trihydrate, pH 6.5, 20% PEG 8000
Resolution 1.55 Å R-free 0.295
5JBV Lys27-linked triubiquitin Deposited 2016-04-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded NO3 NITRATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；291 K；20% (w/v) PEG 3350, 4mM CdCl2, pH 5.9, 200mM Mg(NO3)2
Resolution 2.10 Å R-free 0.306
5JBY Lys27-linked triubiquitin Deposited 2016-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–76（76 aa）
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (w/v) PEG 3350, 4mM CdCl2, pH 5.9, 200mM Mg(NO3)2
Resolution 1.99 Å R-free 0.308
5JG6 APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C Deposited 2016-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 76–154（79 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4.6, 33% PEG4000
Resolution 2.00 Å R-free 0.220
5JG6 APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C Deposited 2016-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 76–154（79 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4.6, 33% PEG4000
Resolution 2.00 Å R-free 0.220
5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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, SITTING DROP；291 K；0.1M CHES (pH 9.5) 1.0M sodium citrate
Resolution 2.90 Å R-free 0.285
5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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, SITTING DROP；291 K；0.1M CHES (pH 9.5) 1.0M sodium citrate
Resolution 2.90 Å R-free 0.285
5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 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, SITTING DROP；291 K；0.1M CHES (pH 9.5) 1.0M sodium citrate
Resolution 2.90 Å R-free 0.285
5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 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, SITTING DROP；291 K；0.1M CHES (pH 9.5) 1.0M sodium citrate
Resolution 2.90 Å R-free 0.285
5JTJ USP7CD-CTP in complex with Ubiquitin Deposited 2016-05-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.05 M Calcium chloride, 0.1 M MES pH 6.0 and 45% PEG 200
Resolution 3.32 Å R-free 0.209
5JTJ USP7CD-CTP in complex with Ubiquitin Deposited 2016-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–76（76 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.05 M Calcium chloride, 0.1 M MES pH 6.0 and 45% PEG 200
Resolution 3.32 Å R-free 0.209
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Chain H 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Chain H 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5K9P Ser20 phosphorylated ubiquitin Deposited 2016-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 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；293 K；45% (w/v) PEG 400, 100 mM tris-HCl
Resolution 1.55 Å R-free 0.219
5KGF Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution Deposited 2016-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain M 1–76（76 aa）
Chain O 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；High concentration NCP-ubme/GST-53BP1 complex at 200 mM salt was diluted just prior to grid freezing.
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Plunged into liquid ethane-propane (FEI VITROBOT MARK III)
Resolution 4.54 Å
5KHY Crystal structure of oxime-linked K6 diubiquitin Deposited 2016-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–73（73 aa）
Chain B 1–75（75 aa）
Mutation：Unnatural aminoxylysine amino acid at position 6 Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：unnatural residue 76 oxime linked to chain A ZN ZINC ION × 10 ETA ETHANOLAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 3350, Zinc acetate
Resolution 3.50 Å R-free 0.331
5KYC Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin (malonate bound) Deposited 2016-07-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded MLA MALONIC ACID × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；8% tacsimate pH 4.0, 20% PEG3350
Resolution 1.43 Å R-free 0.192
5KYD Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin Deposited 2016-07-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；0.2M Ammonium fluoride, 20% PEG3350
Resolution 1.62 Å R-free 0.213
5KYE Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin Deposited 2016-07-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350, 0.2M Ammonium acetate
Resolution 1.97 Å R-free 0.223
5KYE Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin Deposited 2016-07-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350, 0.2M Ammonium acetate
Resolution 1.97 Å R-free 0.223
5KYF Crystal structure of USP7 catalytic domain [L299A] mutant in complex with ubiquitin Deposited 2016-07-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350
Resolution 1.45 Å R-free 0.185
5L8H Structure of USP46-UbVME Deposited 2016-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
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 7.5；293 K；0.96M Sodium Citrate pH7.5 and 0.1mM zinc chloride Cryo - 20% Glycerol
Resolution 1.85 Å R-free 0.194
5L8W Structure of USP12-UB-PRG/UAF1 Deposited 2016-06-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；3.2% PEG4000, 0.1mM MMT pH6.5, 0.1 mM TCEP. Cryo- 30% Glycerol
Resolution 2.79 Å R-free 0.259
5L9T Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with E2 UBE2S poised for polyubiquitination where UBE2S, APC2, and APC11 are modeled into low resolution density Deposited 2016-06-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 22 PDB declaration: 22-meric
Chain S 77–153（77 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
5LN1 STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST; Deposited 2016-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain U 77–152（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION, RECRYSTALLIZATION；pH 6.5；292 K；12% (W/V) PEG 20000, 0.1M MES PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K
Resolution 3.14 Å R-free 0.248
5LRV Structure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diubiquitin Deposited 2016-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–75（75 aa）
Mutation：K11X Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M phosphate citrate (pH 4.2), 20% (w/v) PEG 8K, 0.2 M sodium chloride
Resolution 2.80 Å R-free 0.244
5LRW Structure of Cezanne/OTUD7B OTU domain bound to ubiquitin Deposited 2016-08-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium acetate (pH 4.8), 6% (w/v) PEG 6K
Resolution 2.00 Å R-free 0.217
5LRW Structure of Cezanne/OTUD7B OTU domain bound to ubiquitin Deposited 2016-08-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium acetate (pH 4.8), 6% (w/v) PEG 6K
Resolution 2.00 Å R-free 0.217
5LRX Structure of A20 OTU domain bound to ubiquitin Deposited 2016-08-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76X 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, SITTING DROP；287 K；0.1 M MES/imidazole (pH 6.5), 7% (w/v) PEG 8K, 20% ethylene glycol
Resolution 2.85 Å R-free 0.246
5LRX Structure of A20 OTU domain bound to ubiquitin Deposited 2016-08-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Mutation：G76X 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, SITTING DROP；287 K；0.1 M MES/imidazole (pH 6.5), 7% (w/v) PEG 8K, 20% ethylene glycol
Resolution 2.85 Å R-free 0.246
5M93 Crystal structure of SdeA-modified ubiquitin. Deposited 2016-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 76–152（77 aa）
Mutation：M1S SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
Resolution 1.79 Å R-free 0.231
5M93 Crystal structure of SdeA-modified ubiquitin. Deposited 2016-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 76–152（77 aa）
Mutation：M1S SO4 SULFATE ION × 1 RIB alpha-D-ribofuranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
Resolution 1.79 Å R-free 0.231
5M93 Crystal structure of SdeA-modified ubiquitin. Deposited 2016-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 76–152（77 aa）
Mutation：M1S RIB alpha-D-ribofuranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
Resolution 1.79 Å R-free 0.231
5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 77–152（76 aa）
Not recorded ZN ZINC ION × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
Resolution 2.16 Å R-free 0.231
5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 77–152（76 aa）
Not recorded ZN ZINC ION × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
Resolution 2.16 Å R-free 0.231
5N2W WT-Parkin and pUB complex Deposited 2017-02-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 CL CHLORIDE ION × 1 TMO trimethylamine oxide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100mM Tris pH 8.5, 200mM TMAO, PEG MME 2000
Resolution 2.68 Å R-free 0.243
5N38 S65DParkin and pUB complex Deposited 2017-02-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100mM Tris pH 8.5, 200mM TMAO, PEG MME 2000
Resolution 2.60 Å R-free 0.236
5NL5 Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：E16V ZN ZINC ION × 3 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2
Resolution 1.96 Å R-free 0.237
5NL5 Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：E16V ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2
Resolution 1.96 Å R-free 0.237
5NL5 Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2
Resolution 1.96 Å R-free 0.237
5NLJ Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 4 ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 70 mM Zn(CH3COO)2 and 20% v/v TFE.
Resolution 1.53 Å R-free 0.240
5NLJ Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 1 ZN ZINC ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 ETF TRIFLUOROETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 70 mM Zn(CH3COO)2 and 20% v/v TFE.
Resolution 1.53 Å R-free 0.240
5NLJ Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 70 mM Zn(CH3COO)2 and 20% v/v TFE.
Resolution 1.53 Å R-free 0.240
5NVG Thr12 Phosphorylated Ubiquitin Deposited 2017-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；291.15 K；20% (v/v) ethanol, 20% (w/v) PEG-1000, 0.1M Phosphate-citrate pH 4.2
Resolution 1.07 Å R-free 0.167
5O44 Crystal structure of unbranched mixed tri-Ubiquitin chain containing K48 and K63 linkages. Deposited 2017-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–74（74 aa）
Chain C 1–74（74 aa）
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Mutation：Deleted for Gly 75 and Gly 76 Mutation：Deleted for Gly 75 and Gly 76 Mutation：K48R Mutation：K48R SO4 SULFATE ION × 18 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.3M MgSo4 and 100mM MES monohydrate pH 6.5
Resolution 3.14 Å R-free 0.254
5O6T BIRC4 RING in complex with dimeric ubiquitin variant Deposited 2017-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 75–150（76 aa）
Chain D 75–150（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；291 K；0.1 M NaHEPES pH 7.5, 1.4 M tri-Na citrate
Resolution 1.57 Å R-free 0.183
5OHK Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (high resolution) Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；291 K；10% (w/v) PEG 20000, 0.1 M sodium citrate pH 5.4, 0.2 M lithium sulfate
Resolution 2.34 Å R-free 0.261
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 1–76（76 aa）
Chain N 1–76（76 aa）
Not recorded 15P POLYETHYLENE GLYCOL (N=34) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 1–76（76 aa）
Chain N 1–76（76 aa）
Not recorded 15P POLYETHYLENE GLYCOL (N=34) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–76（76 aa）
Chain M 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–76（76 aa）
Chain M 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain O 1–76（76 aa）
Chain P 1–76（76 aa）
Not recorded 15P POLYETHYLENE GLYCOL (N=34) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHN Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution) Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
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；291 K；20% (w/v) PAA 5100 Na, 100 mM Hepes pH 8.0, 2.5% (v/v) glycerol
Resolution 3.60 Å R-free 0.253
5OHN Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution) Deposited 2017-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
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；291 K；20% (w/v) PAA 5100 Na, 100 mM Hepes pH 8.0, 2.5% (v/v) glycerol
Resolution 3.60 Å R-free 0.253
5OHP Crystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.73 M sodium citrate, 0.1 M Hepes pH 7.0
Resolution 2.80 Å R-free 0.249
5TOF Room temperature structure of ubiquitin variant u7ub25 Deposited 2016-10-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–152（78 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1ul protein solution at 20 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.6, 2.6 M ammonium sulfate)
Resolution 1.12 Å R-free 0.175
5TOG Room temperature structure of ubiquitin variant u7ub25.2540 Deposited 2016-10-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–152（78 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1ul protein solution at 10 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.2, 2.2 M ammonium sulfate)
Resolution 1.08 Å R-free 0.121
5TOG Room temperature structure of ubiquitin variant u7ub25.2540 Deposited 2016-10-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 75–152（78 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1ul protein solution at 10 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.2, 2.2 M ammonium sulfate)
Resolution 1.08 Å R-free 0.121
5TUT UbcH5a-Ub isopeptide conjugate Deposited 2016-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；Hampton PEG/Ion F10
Resolution 2.60 Å R-free 0.243
5UJL Representative 1-conformer ensembles of K27-linked Ub2 from RDC data Deposited 2017-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：residues 1-76
Chain B 1–76（76 aa） Fragment：residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition 150 uM [U-99% 15N] K27-diubiquitin, Distal Ub is 15N-labelled Proximal Ub is not enriched, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 150 uM [U-99% 15N] K27-diubiquitin, Distal Ub is not enriched Proximal Ub is 15N-labelled, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
5UJN Representative 2-conformer ensembles of K27-linked Ub2 from RDC data Deposited 2017-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition 150 uM [U-99% 15N] distal K27-Ub2, 20 mM NaPhosphate, 0.02 % NaN3, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 150 uM [U-99% 15N] proximal K27-Ub2, 20 mM NaPhosphate, 0.02 % NaN3, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
5ULF Crystal Structure of a UbcH5b~Ub conjugate Deposited 2017-01-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
Resolution 1.80 Å R-free 0.261
5ULF Crystal Structure of a UbcH5b~Ub conjugate Deposited 2017-01-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
Resolution 1.80 Å R-free 0.261
5ULH Structure of RNF165 in complex with a UbcH5b~Ub conjugate Deposited 2017-01-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 2 SCN THIOCYANATE ION × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；200 mM potassium thiocyanate, 20% PEG 3350
Resolution 1.95 Å R-free 0.217
5ULK Crystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate Deposited 2017-01-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；200 mM ammonium nitrate, 20% PEG 3350
Resolution 2.38 Å R-free 0.267
5V1Y Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex Deposited 2017-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；277 K；0.1 M citric acid, pH 4.6, 20% PEG6000
Resolution 1.42 Å R-free 0.175
5V1Y Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex Deposited 2017-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；277 K；0.1 M citric acid, pH 4.6, 20% PEG6000
Resolution 1.42 Å R-free 0.175
5V1Z Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex Deposited 2017-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M sodium acetate, pH 4.6, 22.5% PEG3350
Resolution 2.00 Å R-free 0.182
5V1Z Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex Deposited 2017-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M sodium acetate, pH 4.6, 22.5% PEG3350
Resolution 2.00 Å R-free 0.182
5VEY Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A Lys15 in complex with RNF169 (653-708) Deposited 2017-04-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
Resolution not provided
5VF0 Solution NMR structure of human RAD18 (198-240) in complex with ubiquitin Deposited 2017-04-06 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] RAD18, 3 mM Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM RAD18, 0.6 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.9 mM [U-15N] RAD18, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N] RAD18, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.2 mM [U-100% 15N] RAD18, 1.0 mM Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 5 % Alkyl-polyethylene glycol (C12E5)/n-hexanol mixture, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM RAD18, 0.2 mM [U-100% 15N] Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 5 % Alkyl-polyethylene glycol (C12E5)/n-hexanol mixture, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5VNZ Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；289 K；0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350
Resolution 3.41 Å R-free 0.294
5VNZ Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；289 K；0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350
Resolution 3.41 Å R-free 0.294
5VO0 Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 8 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；100-200 mM Na/K tartrate, 11-15% PEG 3350 and 100 mM bis-Tris propane pH 7.5
Resolution 3.90 Å R-free 0.299
5VZM Solution NMR structure of human Rev1 (932-1039) in complex with ubiquitin Deposited 2017-05-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate；Pressure 1
NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate；Pressure 1
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Ubiquitin, 20 mM Sodium phosphate buffer, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Rev1, 3 mM Ubiquitin, 50 mM Sodium phosphate buffer, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM Rev1, 1 mM [U-100% 13C; U-100% 15N] Ubiquitin, 50 mM Sodium phosphate buffer, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5VZW TRIM23 RING domain in complex with UbcH5-Ub Deposited 2017-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.1 M Bis-Tris, pH 5.5, 0.2 M calcium chloride, 17% w/v PEG3350
Resolution 2.28 Å R-free 0.237
5W46 Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution Deposited 2017-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：S65D MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；Tris pH 8.0, magnesium chloride, PEG 3350, Hepes
Resolution 1.18 Å R-free 0.190
5W46 Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution Deposited 2017-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：S65D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；Tris pH 8.0, magnesium chloride, PEG 3350, Hepes
Resolution 1.18 Å R-free 0.190
5WFI X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin Deposited 2017-07-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded GOL GLYCEROL × 5 FMT FORMIC ACID × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；50 mM Tris, pH 7.5, 100 mM sodium chloride, 5 mM DTT, 0.2 M potassium formate, 20% PEG3350
Resolution 1.85 Å R-free 0.197
5WFI X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin Deposited 2017-07-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded GOL GLYCEROL × 5 FMT FORMIC ACID × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；50 mM Tris, pH 7.5, 100 mM sodium chloride, 5 mM DTT, 0.2 M potassium formate, 20% PEG3350
Resolution 1.85 Å R-free 0.197
5X3M crystal structure of p-Ub-S65-NH2 Deposited 2017-02-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 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, SITTING DROP；289 K；0.2M Lithium Sulfate monohydrate, 0.1M HEPES pH 7.5, 25%(w/v) Polyethylene Glycol 3350
Resolution 1.82 Å R-free 0.271
5X3N Crystal structure of DiUb-K6 Deposited 2017-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium formate dihydrate, 20%(w/v) Polyethylene glycol 3350
Resolution 1.65 Å R-free 0.276
5X3O Crystal structure of p-DiUb-S65-COOH Deposited 2017-02-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
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, SITTING DROP；289 K；0.2M Ammonium phosphate monobasic, 20%(w/v) Polyethylene glycol 3350
Resolution 2.19 Å R-free 0.315
5XBO Lanthanoid tagging via an unnatural amino acid for protein structure characterization Deposited 2017-03-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded TB TERBIUM(III) ION × 1 SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 100；Pressure 760
NMR sample composition 20mM HEPES, 100mM sodium chloride, 10% D2O, 0.2mM [U-99% 15N] ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20mM HEPES, 100mM sodium chloride, 0.1mM [U-99% 15N] HHR23A UBA1 Domain, 0.1 mM ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5XDP K11/48-branched teraubiquitin Deposited 2017-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；289 K；0.2M Potassium nitrate, 20% w/v Polyethylene glycol 3350
Resolution 2.38 Å R-free 0.271
5XK4 Retracted state of S65-phosphorylated ubiquitin Deposited 2017-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
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 0.8 mM [U-98% 13C; U-98% 15N] phosphorylated ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5XK5 Relaxed state of S65-phosphorylated ubiquitin Deposited 2017-05-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
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 0.8 mM [U-98% 13C; U-98% 15N] relaxed pUb, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5XPK Crystal structure of ubiquitin-k6mimic Deposited 2017-06-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 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, SITTING DROP；291 K；0.2M Ammonium formate, 20% w/v PEG 3350
Resolution 2.27 Å R-free 0.310
5YIJ Structure of a Legionella effector with substrates Deposited 2017-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain D 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain G 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Not recorded NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 1000, Tris
Resolution 3.18 Å R-free 0.275
5YIK Structure of a Legionella effector with its substrate Deposited 2017-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain D 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain F 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 1000, Tris
Resolution 3.10 Å R-free 0.279
5YMY The structure of the complex between Rpn13 and K48-diUb Deposited 2017-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：K48R No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 0.58 mM [U-13C; U-15N; U-2H] Rpn13, 20 mM MES, 0.15 M sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 77–152（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
Resolution 1.50 Å R-free 0.225
5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 77–152（76 aa）
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
Resolution 1.50 Å R-free 0.225
5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 77–152（76 aa）
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
Resolution 1.50 Å R-free 0.225
5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 77–152（76 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
Resolution 1.50 Å R-free 0.225
5ZBU Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub Deposited 2018-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES monohydrate, 14% PEG 4000
Resolution 3.20 Å R-free 0.262
5ZD0 Solution structure of human ubiquitin with three alanine mutations in living eukaryotic cells by in-cell NMR spectroscopy Deposited 2018-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：L8A,I44A,V70A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 0；300 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR measurement conditions pH 0；300 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR sample composition 50 uM [U-100% 13C; U-100% 15N] human ubiquitin with three alanine mutations 1, 50 uM [U-100% 15N] human ubiquitin with three alanine mutations 2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Mutation：K48R GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
Resolution 2.60 Å R-free 0.236
6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Mutation：K48R GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
Resolution 2.60 Å R-free 0.236
6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–77（77 aa） Fragment：UNP residues 1-77
Mutation：M77D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
Resolution 2.60 Å R-free 0.236
6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–77（77 aa） Fragment：UNP residues 1-77
Mutation：M77D GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
Resolution 2.60 Å R-free 0.236
6ASR REV1 UBM2 domain complex with ubiquitin Deposited 2017-08-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：residues 1-76
Not recorded NI NICKEL (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1 M MES pH 6.0, 10 % PEG 8000
Resolution 2.36 Å R-free 0.229
6ASR REV1 UBM2 domain complex with ubiquitin Deposited 2017-08-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：residues 1-76
Not recorded NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1 M MES pH 6.0, 10 % PEG 8000
Resolution 2.36 Å R-free 0.229
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000
Resolution 2.66 Å R-free 0.263
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000
Resolution 2.66 Å R-free 0.263
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 77–152（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350
Resolution 3.27 Å R-free 0.317
6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 77–152（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350
Resolution 3.27 Å R-free 0.317
6CP2 SidC in complex with UbcH7~Ub Deposited 2018-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 75–152（78 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；16% PEG 3000, 0.1 M Tris pH 9.0
Resolution 2.90 Å R-free 0.288
6DGF Ubiquitin Variant bound to USP2 Deposited 2018-05-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 153–226（74 aa）
Mutation：Q2C, K6C, K11R, T12C ZN ZINC ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M MES buffer pH 6, 12% (w/v) PEG3350, 0.2M sodium sulfate
Resolution 2.34 Å R-free 0.224
6EI1 Crystal structure of the covalent complex between deubiquitinase ZUFSP (ZUP1) and Ubiquitin-PA Deposited 2017-09-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 GOL GLYCEROL × 1 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；277 K；0.2 M sodium malonate pH 5, 20 % PEG 3350
Resolution 1.73 Å R-free 0.203
6FGE Crystal structure of human ZUFSP/ZUP1 in complex with ubiquitin Deposited 2018-01-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MLI MALONATE ION × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 2 FMT FORMIC ACID × 7 PEG DI(HYDROXYETHYL)ETHER × 1 NH4 AMMONIUM ION × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；4% v/v Tacsimate pH 5.0 and 12% w/v Polyethylene glycol 3,350.
Resolution 1.74 Å R-free 0.209
6FTX Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain N 1–76（76 aa）
Chain O 1–76（76 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6FX4 Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C Deposited 2018-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76C GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.36M tri-Sodium citrat pH6.5, 15% (v/v) Glycerol
Resolution 2.50 Å R-free 0.239
6FX4 Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C Deposited 2018-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Mutation：G76C GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.36M tri-Sodium citrat pH6.5, 15% (v/v) Glycerol
Resolution 2.50 Å R-free 0.239
6FYH Disulfide between ubiquitin G76C and the E3 HECT ligase Huwe1 Deposited 2018-03-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76C SO4 SULFATE ION × 2 ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.8M Zn SO4 0.1M Na Acetat pH 4.0
Resolution 2.91 Å R-free 0.266
6GLC Structure of phospho-Parkin bound to phospho-ubiquitin Deposited 2018-05-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 GOL GLYCEROL × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.03 M of each sodium nitrate, disodium hydrogen phosphate, ammonium sulphate, 0.1 M MOPS/HEPES-Na (pH 7.5)
Resolution 1.80 Å R-free 0.205
6GZS Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to ubiquitin Deposited 2018-07-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded GOL GLYCEROL × 1 SO4 SULFATE ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MES (pH 6.0), 20% PEG 6000
Resolution 1.90 Å R-free 0.213
6H4H Usp28 catalytic domain variant E593D in complex with UbPA Deposited 2018-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–75（75 aa）
Chain D 1–75（75 aa）
Not recorded SO4 SULFATE ION × 1 AYE prop-2-en-1-amine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；273 K；0.1 M Citrate pH 5.0 0.8 M Ammonium Sulfate
Resolution 3.50 Å R-free 0.280
6HEI Structure of the catalytic domain of USP28 (insertion deleted) bound to Ubiquitin-PA Deposited 2018-08-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–151（75 aa）
Mutation：residue 76 replaced with PA warhead Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；22% (w/v) PEG 3350, 300 mM potassium sodium tartrate
Resolution 1.64 Å R-free 0.214
6HEK Structure of human USP28 bound to Ubiquitin-PA Deposited 2018-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 77–152（76 aa）
Chain D 77–152（76 aa）
Mutation：residue 76 replaced with PA warhead Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：residue 76 replaced with PA warhead Non-standard monomer：Yes (specific site not provided by mmCIF) PG4 TETRAETHYLENE GLYCOL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；291 K；8% (w/v) PEG 3350, 200 mM ammonium acetate and 100 mM sodium citrate pH 5.4
Resolution 3.03 Å R-free 0.237
6HPR Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub Deposited 2018-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 75–152（78 aa）
Chain D 75–152（78 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M ammonium fluoride and 15% (w/v) PEG 3350
Resolution 1.70 Å R-free 0.197
6IF1 Crystal structure of Ube2K and K48-linked di-ubiquitin complex Deposited 2018-09-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；Tris-HCl, polyethylene glycol 3350, ammonium acetate.
Resolution 2.47 Å R-free 0.236
6IF1 Crystal structure of Ube2K and K48-linked di-ubiquitin complex Deposited 2018-09-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；Tris-HCl, polyethylene glycol 3350, ammonium acetate.
Resolution 2.47 Å R-free 0.236
6ISU Crystal structure of Lys27-linked di-ubiquitin in complex with its selective interacting protein UCHL3 Deposited 2018-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–76（76 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；291.15 K；18% PEG 3350 (w/v), 400 mM Ca(AC)2
Resolution 1.87 Å R-free 0.264
6JB6 Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.7 A resolution Deposited 2019-01-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, PEG 400, magnesium chloride
Resolution 2.70 Å R-free 0.284
6JB7 Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.1 A resolution Deposited 2019-01-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, PEG 400, magnesium chloride
Resolution 2.10 Å R-free 0.250
6JMA cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Deposited 2019-03-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain Y 1–76（76 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6K9P Structure of Deubiquitinase Deposited 2019-06-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350
Resolution 2.05 Å R-free 0.210
6LP2 Structure of Lpg2148/UBE2N-Ub complex Deposited 2020-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, potassium citrate
Resolution 2.48 Å R-free 0.233
6MSB Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Chain w 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6MSD Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Chain w 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6MSE Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6MSG Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N13 UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin Deposited 2018-11-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Not recorded ZN ZINC ION × 8 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.11 mM [U-13C; U-15N; U-2H] UbcH7, 0.11 mM [U-13C; U-15N; U-2H] ubiquitin, 0.11 mM [U-2H] Parkin -residues 144-465 comprising the RING0-RING1-IBR and RING2(Rcat) domains, 0.11 mM [U-2H] phosphorylated ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6NJ9 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Deposited 2019-01-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain L 1–76（76 aa）
Chain N 1–76（76 aa）
Mutation：G76C Mutation：G76C SAM S-ADENOSYLMETHIONINE × 2 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 2.96 Å
6OQ1 Crystal Structure of Branched K11/K48-Linked Tri-Ubiquitin Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain C 1–76（76 aa）
Chain F 1–77（77 aa）
Mutation：K11R, K48C, K63R Mutation：K48R Mutation：M77D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；bis-tris, sodium chloride, PEG 3350
Resolution 2.20 Å R-free 0.230
6OQ1 Crystal Structure of Branched K11/K48-Linked Tri-Ubiquitin Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–77（77 aa）
Mutation：K11R, K48C, K63R Mutation：K48R Mutation：M77D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；bis-tris, sodium chloride, PEG 3350
Resolution 2.20 Å R-free 0.230
6OQ2 NMR Structure of Branched K11/K48-Linked Tri-Ubiquitin Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–77（77 aa）
Mutation：K11R, K48R, K63R Mutation：K48R Mutation：M77D No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 120 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 100 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 60 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 110 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6PGV Human Josephin-2 in complex with ubiquitin Deposited 2019-06-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 4.6；293 K；0.1 M sodium acetate pH 4.6, 0.2 M CaCl2, 22.5% (w/v) PEG 6000; microbatch under Al's Oil
Resolution 2.30 Å R-free 0.224
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 77–150（74 aa）
Chain B 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 77–150（74 aa）
Chain D 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 77–150（74 aa）
Chain F 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 77–150（74 aa）
Chain H 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain I 77–150（74 aa）
Chain J 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain K 77–150（74 aa）
Chain L 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QML UCHL3 in complex with synthetic, K27-linked diubiquitin Deposited 2019-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Mutation：M1(NLE) Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 2 BR BROMIDE ION × 3 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops. Best crystals: 21% PEG 3350 0.15M KBr 0.1M Bis-Tris pH 5.5 Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.
Resolution 2.10 Å R-free 0.233
6QML UCHL3 in complex with synthetic, K27-linked diubiquitin Deposited 2019-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Mutation：M1(NLE) Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 3 BR BROMIDE ION × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops. Best crystals: 21% PEG 3350 0.15M KBr 0.1M Bis-Tris pH 5.5 Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.
Resolution 2.10 Å R-free 0.233
6UD0 Solution-state NMR structural ensemble of human Tsg101 UEV in complex with K63-linked diubiquitin Deposited 2019-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–77（77 aa）
Mutation：K63R Mutation：+D77 No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；300 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1
NMR sample composition 200 uM [U-98% 15N] Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM Tsg101 UEV domain, 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM [U-98% 15N] Tsg101 UEV domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
6UYI hRpn13:hRpn2:K48-diubiquitin Deposited 2019-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–77（77 aa）
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298.15 K；Ionic strength (raw mmCIF value) 0.11；Pressure ambient
NMR sample composition 0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2O | 100% D2O
NMR sample composition 0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM proximal ubiquitin, 0.72 mM [U-13C] distal ubiquitin, 100% D2O | 100% D2O
Resolution not provided
6UYJ hRpn13:hRpn2:K48-diubiquitin Deposited 2019-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–77（77 aa）
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298.15 K；Ionic strength (raw mmCIF value) 0.11；Pressure ambient
NMR sample composition 0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2O | 100% D2O
NMR sample composition 0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2O | 100% D2O
Resolution not provided
6XZ1 Conjugate of the HECT domain of HUWE1 with ubiquitin Deposited 2020-01-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Not recorded PO4 PHOSPHATE ION × 2 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.65 M Sodium phosphate monobasic, potassium phosphate dibasic, 0.1 M HEPES pH 7.5
Resolution 2.30 Å R-free 0.255
6XZ1 Conjugate of the HECT domain of HUWE1 with ubiquitin Deposited 2020-01-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded PO4 PHOSPHATE ION × 3 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.65 M Sodium phosphate monobasic, potassium phosphate dibasic, 0.1 M HEPES pH 7.5
Resolution 2.30 Å R-free 0.255
7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain CCC 75–152（78 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
Resolution 1.82 Å R-free 0.231
7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain FFF 75–152（78 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
Resolution 1.82 Å R-free 0.231
7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain III 75–152（78 aa）
Not recorded ZN ZINC ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
Resolution 1.82 Å R-free 0.231
7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain LLL 75–152（78 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
Resolution 1.82 Å R-free 0.231
7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain CCC 75–152（78 aa）
Not recorded CL CHLORIDE ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
Resolution 1.56 Å R-free 0.185
7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain FFF 75–152（78 aa）
Not recorded CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
Resolution 1.56 Å R-free 0.185
7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain CCC 75–152（78 aa）
Not recorded CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
Resolution 2.07 Å R-free 0.266
7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain FFF 75–152（78 aa）
Not recorded CL CHLORIDE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
Resolution 2.07 Å R-free 0.266
7AY2 Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg Deposited 2020-11-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 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；292 K；8-13% w/v PEG3350, 0.1 M citric acid/Bis-Tris propane pH 4.1
Resolution 3.20 Å R-free 0.234
7AY2 Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg Deposited 2020-11-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；8-13% w/v PEG3350, 0.1 M citric acid/Bis-Tris propane pH 4.1
Resolution 3.20 Å R-free 0.234
7CAP Cyclic Lys48-linked triubiquitin Deposited 2020-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；20% PEG 3350, 200 mM zinc acetate
Resolution 1.33 Å R-free 0.174
7DNI MDA5 CARDs-MAVS CARD polyUb complex Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Chain H 1–76（76 aa）
Chain I 1–76（76 aa）
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Chain L 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 3.20 Å
7DNJ K63-polyUb MDA5CARDs complex Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Chain H 1–76（76 aa）
Chain I 1–76（76 aa）
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Chain L 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 OTHER
Resolution 3.30 Å
7F7X Protein complex between phosphorylated ubiquitin and Ubqln2 UBA Deposited 2021-06-30 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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 1
NMR sample composition 20 mM HEPES, 0.15 M sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded CA CALCIUM ION × 3 AYE prop-2-en-1-amine × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
Resolution 2.78 Å R-free 0.273
7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded CA CALCIUM ION × 3 AYE prop-2-en-1-amine × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
Resolution 2.78 Å R-free 0.273
7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded CA CALCIUM ION × 2 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
Resolution 2.78 Å R-free 0.273
7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Not recorded CA CALCIUM ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
Resolution 2.78 Å R-free 0.273
7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 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 2.94 Å
7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT
Resolution 2.47 Å R-free 0.276
7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT
Resolution 2.47 Å R-free 0.276
7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Not recorded GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT
Resolution 2.47 Å R-free 0.276
7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa）
Not recorded GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT
Resolution 2.47 Å R-free 0.276
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 3 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 3 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Not recorded ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 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；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 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；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 1–75（75 aa）
Not recorded ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 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；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MEY Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron Deposited 2021-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–75（75 aa） Fragment：K48C
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 7 Z3V 2-(ethylamino)ethane-1-thiol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.67 Å
7MYF Ubiquitin variant UbV.k.1 in complex with Ube2k Deposited 2021-05-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Mutation：Q31F, G21R, T23Y, A57S, K59Q, K74E, E75F, T77F, V81I, L82S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2-0.3 M ammonium citrate dibasic, 20-25% PEG3350
Resolution 3.00 Å R-free 0.293
7MYH Ubiquitin variant UbV.k.2 in complex with Ube2k Deposited 2021-05-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Mutation：K6S, L8F, T9V, K11L, T14M, K63N, E64D, T66I, H68R, L71I, G76L GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M sodium citrate tribasic trihydrate, 0.1 M Bis-Tris propane, pH 7.5, 20% PEG3350
Resolution 2.39 Å R-free 0.249
7OJE Crystal structure of the covalent complex between Tribolium castaneum deubiquitinase ZUP and Ubiquitin-PA Deposited 2021-05-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8 % (v/v) Tacsimate pH 7; 22 %PEG3350
Resolution 2.05 Å R-free 0.219
7OJE Crystal structure of the covalent complex between Tribolium castaneum deubiquitinase ZUP and Ubiquitin-PA Deposited 2021-05-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8 % (v/v) Tacsimate pH 7; 22 %PEG3350
Resolution 2.05 Å R-free 0.219
7OJX E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for K48-linked Ub chain synthesis Deposited 2021-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Mutation：K48C ZN ZINC ION × 2 ME7 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；Crystals were grown in: 0.2 M sodium citrate, 0.1 M Bis Tris propane 7.5 and 20 % (w/v) PEG 3350. The crystallization drops were set as a 1:1 mixture of the protein complex solution and the precipitant solution.
Resolution 2.40 Å R-free 0.236
7QO5 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state Deposited 2021-12-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
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 6.00 Å
7RBR The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with a Lys48-linked di-ubiquitin Deposited 2021-07-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–77（77 aa）
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.2 M di-sodium tartrate, 20% PEG-3350,
Resolution 1.88 Å R-free 0.228
7RMA Structure of the fourth UIM (Ubiquitin Interacting Motif) of ANKRD13D in complex with a high affinity UbV (Ubiquitin Variant) Deposited 2021-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–79（79 aa）
Not recorded SO4 SULFATE ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1M Li2SO4, 0.1M sodium acetate pH 4.5 and 50% PEG 400. Crystals were cryoprotected in this buffer plus 20% ethylene glycol
Resolution 2.00 Å R-free 0.246
7S6O The crystal structure of Lys48-linked di-ubiquitin Deposited 2021-09-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：K48R Mutation：Aspartic acid residue added to C terminus (D77) ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；289 K；50 mM acetate, 8.6% PEG2000 MME, 17.1% PEG400
Resolution 1.25 Å R-free 0.175
7UV5 The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a Lys48-linked di-ubiquitin Deposited 2022-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Mutation：K48R ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.2 M sodium tartrate, 15% PEG3350
Resolution 1.45 Å R-free 0.179
7W38 Structure of USP14-bound human 26S proteasome in state EA2.0_UBL Deposited 2021-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7W39 Structure of USP14-bound human 26S proteasome in state EA2.1_UBL Deposited 2021-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain u 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7W3A Structure of USP14-bound human 26S proteasome in substrate-engaged state ED4_USP14 Deposited 2021-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7W3B Structure of USP14-bound human 26S proteasome in substrate-engaged state ED5_USP14 Deposited 2021-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7W3C Structure of USP14-bound human 26S proteasome in substrate-engaged state ED0_USP14 Deposited 2021-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7W3F Structure of USP14-bound human 26S proteasome in substrate-engaged state ED1_USP14 Deposited 2021-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7W3G Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.0_USP14 Deposited 2021-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7W3H Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.1_USP14 Deposited 2021-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7W3I Structure of USP14-bound human 26S proteasome in substrate-inhibited state SB_USP14 Deposited 2021-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7W3J Structure of USP14-bound human 26S proteasome in substrate-inhibited state SC_USP14 Deposited 2021-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
7W3K Structure of USP14-bound human 26S proteasome in substrate-inhibited state SD4_USP14 Deposited 2021-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7W3M Structure of USP14-bound human 26S proteasome in substrate-inhibited state SD5_USP14 Deposited 2021-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7XCR Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex Deposited 2022-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
7XCT Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex Deposited 2022-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain L 1–76（76 aa）
Chain N 1–76（76 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8BS9 Structure of USP36 in complex with Ubiquitin-PA Deposited 2022-11-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.3 M potassium formate, 14% (w/v) PEG 3350
Resolution 1.90 Å R-free 0.209
8BS9 Structure of USP36 in complex with Ubiquitin-PA Deposited 2022-11-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.3 M potassium formate, 14% (w/v) PEG 3350
Resolution 1.90 Å R-free 0.209
8C07 Structure of HECT E3 UBR5 forming K48 linked Ubiquitin chains Deposited 2022-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–76（76 aa）
Chain K 1–76（76 aa）
Not recorded SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8C61 Structure of USP54 in complex with Lys63-linked diUbiquitin-PA Deposited 2023-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–75（75 aa）
Chain C 1–76（76 aa）
Chain E 1–75（75 aa）
Chain F 1–76（76 aa）
Mutation：K63R Mutation：K63R ZN ZINC ION × 6 AYE prop-2-en-1-amine × 2 CL CHLORIDE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；27.2 % (v/v) PEG 400, 0.1 M HEPES, 0.2 M calcium chloride
Resolution 2.50 Å R-free 0.243
8C61 Structure of USP54 in complex with Lys63-linked diUbiquitin-PA Deposited 2023-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain H 1–75（75 aa）
Chain I 1–76（76 aa）
Chain K 1–75（75 aa）
Chain L 1–76（76 aa）
Mutation：K63R Mutation：K63R ZN ZINC ION × 6 AYE prop-2-en-1-amine × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；27.2 % (v/v) PEG 400, 0.1 M HEPES, 0.2 M calcium chloride
Resolution 2.50 Å R-free 0.243
8DMQ Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester Deposited 2022-07-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Not recorded FLC CITRATE ANION × 4 EDO 1,2-ETHANEDIOL × 2 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.19 Å R-free 0.209
8DMQ Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester Deposited 2022-07-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded FLC CITRATE ANION × 1 EDO 1,2-ETHANEDIOL × 1 GVE METHYL 4-AMINOBUTANOATE × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.19 Å R-free 0.209
8DMS Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose Deposited 2022-07-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Not recorded 1PE PENTAETHYLENE GLYCOL × 1 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.15 Å R-free 0.207
8DMS Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose Deposited 2022-07-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded 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 GVE METHYL 4-AMINOBUTANOATE × 1 FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.15 Å R-free 0.207
8EFW Structure of SdeA DUB Domain disulfide crosslinked with Ubiquitin Deposited 2022-09-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；2.8M sodium acetate: HCl pH7
Resolution 2.81 Å
8EFX Structure of OtDUB DUB Domain disulfide crosslinked with Ubiquitin Deposited 2022-09-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.16M Magnesium chloride, 0.08M Tris at pH 8.5, 24% PEG 8000 and 20% glycerol
Resolution 1.85 Å R-free 0.229
8EHO PRRSV-1 PLP2 domain bound to ubiquitin Deposited 2022-09-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 2 3CN 3-AMINOPROPANE × 1 NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2M Mg(NO3)2
Resolution 2.85 Å R-free 0.247
8EHO PRRSV-1 PLP2 domain bound to ubiquitin Deposited 2022-09-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 3 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2M Mg(NO3)2
Resolution 2.85 Å R-free 0.247
8EHO PRRSV-1 PLP2 domain bound to ubiquitin Deposited 2022-09-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 2 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2M Mg(NO3)2
Resolution 2.85 Å R-free 0.247
8F1F Structure of K48-linked tri-ubiquitin in complex with cyclic peptide Deposited 2022-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：D77 added to the C-terminus Mutation：K48R GOL GLYCEROL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Droplets were formed by mixing equal volumes of Ub3:Ub4a complex (8 mg/ml) and the crystallization solution containing 0.15 M NaCl, 23% (w/v) PEG 3350 and 0.1 M HEPES (pH 7.5)
Resolution 1.85 Å R-free 0.298
8F1F Structure of K48-linked tri-ubiquitin in complex with cyclic peptide Deposited 2022-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain a 1–76（76 aa）
Chain b 1–76（76 aa）
Chain c 1–76（76 aa）
Mutation：D77 added to the C-terminus Mutation：K48R EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Droplets were formed by mixing equal volumes of Ub3:Ub4a complex (8 mg/ml) and the crystallization solution containing 0.15 M NaCl, 23% (w/v) PEG 3350 and 0.1 M HEPES (pH 7.5)
Resolution 1.85 Å R-free 0.298
8G6G H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5 Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 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 2.93 Å
8G6H H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6 Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 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 3.06 Å
8G6Q H2AK119ub-modified nucleosome ubiquitin position 1 Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 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 3.41 Å
8G6S H2AK119ub-modified nucleosome ubiquitin position 2 Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 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 3.47 Å
8GRM Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Deposited 2022-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain O 1–76（76 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
8H1T Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Deposited 2022-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain M 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8IC9 Lys48-linked K48C-diubiquitin Deposited 2023-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：K48C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；38% 2-methyl-2,4-pentanediol and 50 mM sodium citrate (pH 4.0)
Resolution 1.25 Å R-free 0.219
8IC9 Lys48-linked K48C-diubiquitin Deposited 2023-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Mutation：K48C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；38% 2-methyl-2,4-pentanediol and 50 mM sodium citrate (pH 4.0)
Resolution 1.25 Å R-free 0.219
8ITP Crystal structure of USP47 catalytic domain complex with ubiquitin Deposited 2023-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM bis-Tris (pH 5.5), 25% PEG 3350, 50 mM MgCl2
Resolution 3.00 Å R-free 0.284
8ITP Crystal structure of USP47 catalytic domain complex with ubiquitin Deposited 2023-03-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM bis-Tris (pH 5.5), 25% PEG 3350, 50 mM MgCl2
Resolution 3.00 Å R-free 0.284
8J1P Cryo-EM structure of Ufd4 in complex with K29/48 triUb Deposited 2023-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Mutation：K29C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8JRT Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) bound to K11/K48-branched ubiquitin (Ub) chain composed of three Ub. Deposited 2023-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain u 77–152（76 aa）
Chain v 77–152（76 aa）
Chain w 77–152（76 aa）
Mutation：K63R Mutation：K63R Mutation：K63R ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；incubation time= 3 s blotting time= 2.5 s
Resolution 3.60 Å
8JTI Cryo-EM structure of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub. Deposited 2023-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 29 PDB declaration: 29-meric
Chain u 77–152（76 aa）
Chain v 77–152（76 aa）
Chain w 77–152（76 aa）
Chain x 77–152（76 aa）
Mutation：K63R Mutation：K63R Mutation：K63R Mutation：K63R ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；incubation time= 3 s blotting time= 2.5 s
Resolution 3.80 Å
8K0G Cryo-EM structure of human 26S RP (Ed state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub. Deposited 2023-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain u 77–152（76 aa）
Chain v 77–152（76 aa）
Chain w 77–152（76 aa）
Chain x 77–152（76 aa）
Mutation：K63R Mutation：K63R Mutation：K63R Mutation：K63R ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；incubation time= 3 s blotting time= 2.5 s
Resolution 3.80 Å
8K6F LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 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；PEG8000, Sodium Choride, Sodium HEPES
Resolution 3.41 Å R-free 0.243
8K6R LnaB-Actin-PRUb ternary complex in the presence of AMPPNP Deposited 2023-07-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 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；Sodium Chloride, Sodium HEPES, PEG8000
Resolution 2.76 Å R-free 0.261
8K6V LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 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；Magnesium acetate, MOPS, PEG8000
Resolution 2.60 Å R-free 0.307
8OYP Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic Deposited 2023-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded CD CADMIUM ION × 1 CL CHLORIDE ION × 1 NO3 NITRATE ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；100 mM Tris/Bicine pH 8.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 11.25% v/v MPD; 11.25% PEG 1000; 11.25% w/v PEG 3350 with 5 mM CdCl2
Resolution 2.44 Å R-free 0.235
8OYP Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic Deposited 2023-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded CD CADMIUM ION × 1 CL CHLORIDE ION × 1 NO3 NITRATE ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；100 mM Tris/Bicine pH 8.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 11.25% v/v MPD; 11.25% PEG 1000; 11.25% w/v PEG 3350 with 5 mM CdCl2
Resolution 2.44 Å R-free 0.235
8Q00 TssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430) reacted with Ub-PA Deposited 2023-07-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium citrate dibasic and 22 % w/v PEG 3350; 1:2, 1:1, 2:1 protein:reservoir ration; cryoprotected with reservoir + 25% ethylene glycol
Resolution 1.62 Å R-free 0.198
8Q00 TssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430) reacted with Ub-PA Deposited 2023-07-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium citrate dibasic and 22 % w/v PEG 3350; 1:2, 1:1, 2:1 protein:reservoir ration; cryoprotected with reservoir + 25% ethylene glycol
Resolution 1.62 Å R-free 0.198
8RQI Structure of Rhizobium NopD with ubiquitin Deposited 2024-01-18 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M imidazole 8.0 and 10% PEG8000
Resolution 1.94 Å R-free 0.199
8RX0 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub Deposited 2024-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain U 1–76（76 aa）
Not recorded 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 18–76（59 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 18–76（59 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 18–76（59 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8V25 H2BK120ub-modified nucleosome ubiquitin position 1 Deposited 2023-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 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 3.32 Å
8V26 H2BK120ub-modified nucleosome ubiquitin position 2 Deposited 2023-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 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 3.33 Å
8V27 H2BK120ub-modified nucleosome ubiquitin position 3 Deposited 2023-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 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 3.34 Å
8V28 H2BK120ub-modified nucleosome ubiquitin position 4 Deposited 2023-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 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 3.36 Å
8W31 Crystal structure of parkin (R0RB):2pUb with activator compound Deposited 2024-02-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–75（75 aa） Fragment：residues 1-75
Chain C 1–75（75 aa） Fragment：residues 1-75
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 A1AE9 (S)-1-(6-benzyl-3-(4-(1,2,3,4-tetrahydroquinoline-1-carbonyl)phenyl)-6,7-dihydropyrazolo[1,5-a]pyrazin-5(4H)-yl)ethan-1-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M Sodium Chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350
Resolution 2.50 Å R-free 0.294
8XEP Crystal structure of a Legionella pneumophila type IV effector in complex with ubiquitin Deposited 2023-12-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；100 mM sodium acetate, pH 6.0, 160 mM ammonium sulfate, 21% PEG 4000, 20% glycerol
Resolution 2.95 Å R-free 0.228
9AVT Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin Deposited 2024-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded SO4 SULFATE ION × 4 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.2 M ammonium sulphate
Resolution 1.50 Å R-free 0.203
9AVW Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin Deposited 2024-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–152（152 aa）
Chain B 1–152（152 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；2.2 M ammonium sulphate, 20% glycerol
Resolution 1.75 Å R-free 0.222
9AZJ Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1 Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain F 1–76（76 aa）
Chain S 1–76（76 aa）
Chain Z 1–76（76 aa）
Mutation：G76C Mutation：G76C Mutation：G76C ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.6；293 K；150nl protein + 50 nl mother liquor: 0.1 M Tris/Bicine pH 8.6, 24.2% PEG 500 MME, 8% PEG 20K, 0.03 M each of NaI, NaBr, and NaF. Cryoprotected in mother liquor containing 20% glycerol
Resolution 3.32 Å R-free 0.285
9B0Z Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 2 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 heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–152（152 aa）
Chain D 1–152（152 aa）
Chain G 1–152（152 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；20% PEG 2K MME, 0.2 M TAO and 0.1 M Tris pH 8.5. Cryoprotected in mother liquor containing 20% glycerol
Resolution 2.41 Å R-free 0.270
9B12 Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1 Deposited 2024-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–152（152 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；3:1 with reservoir solution containing 50% PEG 200 and 0.1 M HEPES pH 7.5
Resolution 1.81 Å R-free 0.269
9B12 Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1 Deposited 2024-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–152（152 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；3:1 with reservoir solution containing 50% PEG 200 and 0.1 M HEPES pH 7.5
Resolution 1.81 Å R-free 0.269
9C5E Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin Deposited 2024-06-06 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 300 uM [U-13C; U-15N] Rcat domain from Parkin, 300 uM Ubiquitin G75-C3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 800 uM [U-13C; U-15N] Rcat domain from Parkin, 800 uM Ubiquitin G75-C3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 300 uM [U-13C; U-15N] Ubiquitin G75-C3, 300 uM Rcat domain from Parkin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 300 uM [U-13C; U-15N] Rcat domain from Parkin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 500 uM [U-13C; U-15N] Ubiquitin G75-C3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
9D1I Structure of Ubiquitin bound to KLHDC3-EloB/C Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；10%PEG5KMME, 0.1M HEPES pH=7.0, 5% Tascsimate pH=7.0
Resolution 2.00 Å R-free 0.189
9DBY ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Deposited 2024-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain N 1–76（76 aa）
Mutation：G76C 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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain N 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9DG3 ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome Deposited 2024-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain N 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9EBS Cryo-EM structure of USP1-UAF1-Ubiquitin in complex with TNG348 Deposited 2024-11-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded A1A4Y 3-(methanesulfonyl)propan-1-amine × 1 ZN ZINC ION × 1 A1BHF 2-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-9-({4-[1-methyl-4-(trifluoromethyl)-1H-imidazol-2-yl]phenyl}methyl)-7-(2,2,2-trifluoroethyl)-7,9-dihydro-8H-purin-8-imine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EMK DupA from legionella covalently bound to ubiquitin-based probe Deposited 2024-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1H50 [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000 0.1 M HEPES pH7 0.2 M MgCl2
Resolution 2.17 Å R-free 0.239
9EMK DupA from legionella covalently bound to ubiquitin-based probe Deposited 2024-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1H50 [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000 0.1 M HEPES pH7 0.2 M MgCl2
Resolution 2.17 Å R-free 0.239
9EMK DupA from legionella covalently bound to ubiquitin-based probe Deposited 2024-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1H50 [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000 0.1 M HEPES pH7 0.2 M MgCl2
Resolution 2.17 Å R-free 0.239
9F5T Ubiquitin C-terminal clippase BpJOS Deposited 2024-04-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–152（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1 M CHES pH 9.5; 22 % PEG 8000; 1:2 protein reservoir drop ration; cryoprotected with reservoir + 20% Glycerol
Resolution 2.56 Å R-free 0.253
9F5T Ubiquitin C-terminal clippase BpJOS Deposited 2024-04-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–152（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1 M CHES pH 9.5; 22 % PEG 8000; 1:2 protein reservoir drop ration; cryoprotected with reservoir + 20% Glycerol
Resolution 2.56 Å R-free 0.253
9F6G Human USP30 chimera bound to Ubiquitin-PA Deposited 2024-05-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.56 M sodium citrate pH 7.0
Resolution 1.50 Å R-free 0.211
9FN4 DUBS Parachlamydia sp. PcJOS Deposited 2024-06-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–152（152 aa）
Not recorded TLA L(+)-TARTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Molecular Dimensions Morpheus B7, 298 K.
Resolution 2.15 Å R-free 0.201
9FPA DUBS Parachlamydia sp. PcJOS orthorhombic crystal form Deposited 2024-06-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–152（152 aa）
Not recorded CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Midas G6. 35 % v/v glycerol ethoxylate, 0.2 M lithium citrate
Resolution 2.18 Å R-free 0.212
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain V 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9GKM Structure of HECT E3 TRIP12 forming K29/K48-branched Ubiquitin chains Deposited 2024-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Mutation：K48R SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.69 Å
9HNW USP1-UAF1 bound to Lys63-linked diubiquitin Deposited 2024-12-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–75（75 aa）
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K63(DAB) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
9ISZ Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 153–228（76 aa）
Chain D 153–228（76 aa）
Mutation：G76C Mutation：G76C SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0
Resolution 2.60 Å R-free 0.274
9ISZ Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 153–228（76 aa）
Mutation：G76C SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0
Resolution 2.60 Å R-free 0.274
9ISZ Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 153–228（76 aa）
Mutation：G76C SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0
Resolution 2.60 Å R-free 0.274
9MC6 Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 2 Deposited 2025-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9MC7 Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 4 Deposited 2025-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9MC9 Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 1 Deposited 2025-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
9MCB Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 1 Deposited 2025-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
9QHI Structure of UBA6-UbDha-BIRC6 trapped ternary complex (cluster 0) Deposited 2025-03-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
9QUG Structure of a UBC-Ubiquitin conjugate Deposited 2025-04-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded GOL GLYCEROL × 4 P4K polyethylene glycol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% (w/v) Polyethylene glycol monomethyl ether 2,000
Resolution 1.80 Å R-free 0.192
9V33 Calypso/Asx/NCP-ub complex Deposited 2025-05-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain M 77–151（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 5.90 Å
9V9Q Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain O 153–228（76 aa）
Mutation：G76C 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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain O 153–228（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
9V9S Cryo-EM structure of the ncPRC1.1 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 153–228（76 aa）
Chain O 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.80 Å
9V9T Cryo-EM structure of the ncPRC1.6 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 153–228（76 aa）
Chain O 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.90 Å
9V9U Cryo-EM structure of the ncPRC1.4 complex containing two RNF2-BMI1 bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain O 153–228（76 aa）
Chain P 153–228（76 aa）
Mutation：G76C Mutation：G76C 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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain K 153–228（76 aa）
Chain O 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.80 Å
9V9W Cryo-EM structure of the ncPRC1.4 complex containing two RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 153–228（76 aa）
Chain O 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 153–228（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
9V9Z Cryo-EM structure of the ncPRC1.4 complex containing one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain O 153–228（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain O 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain O 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.63 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain O 1–76（76 aa）
Chain U 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain O 1–76（76 aa）
Chain U 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

278 other PDB entries and 429 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBB_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–75； UniProt 1–75

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

SAXS scattering curve SAXS Profile

SAXS profile for 6fdk

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6fdk
Deposition date deposition_date2017-12-25
Structure title titleStructure of Chlamydia trachomatis effector protein Cdu1 bound to ubiquitin
Keywords keywordsChlaDUB1, CE protease, DUB, Ubiquitin., HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.75 Å
Radius of gyration Rg (electron density) rg_electron20.38 Å
Forward intensity I(0) i020880500.00
Molecular weight molecular_weight36160.0 kDa
Excluded volume excluded_volume45911 ų
Envelope volume envelope_volume54323 ų
Hydration-shell volume shell_volume22302 ų
Envelope diameter envelope_diameter69.0 Å
Shell Rg shell_rg27.09 Å
Envelope Rg envelope_rg20.58 Å
Shape Rg shape_rg20.36 Å
Total Rg total_rg21.36 Å
Total atoms total_atoms2548
Residues n_residues317
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax67.9 Å
Rg (real space) rg_real21.65 Å
Rg uncertainty (real space) rg_real_error0.32 Å
I(0) (real space) i0_real2.0880e+07
I(0) uncertainty (real space) i0_real_error2.6100e+05
Rg (reciprocal space) rg_reciprocal21.67 Å
I(0) (reciprocal space) i0_reciprocal20880000.0000
Solution quality estimate total_estimate0.9025
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.4 Å
Skewness Skewness skewness0.236
Kurtosis Kurtosis kurtosis-0.353
Angular range angular_range— – 0.3650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5141000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.995
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6fdkb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
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8. Citations (1)

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9. Files and Curves (10)