Ubiquitin
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 76–152 | Not recorded | No other associated polymer | SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.3；Pressure ambient NMR sample composition：1 mM [U-99% 13C; U-99% 15N] sodium phosphate-1, 90% H2O/10% D2O | 90% H2O/10% D2O | Resolution not provided |
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 2LD9 | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 11SY Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused) Deposited 2026-03-11 | 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 × 6 PDB declaration: hexameric |
Chain H
1–76（76 aa）
Chain I
1–76（76 aa）
Chain J
1–76（76 aa）
Chain K
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6；50 mM HEPES, pH 7.6, 150 mM KCl, 5 mM MgCl2, 2 mM ATP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.28 Å |
| 1OGW Synthetic Ubiquitin with fluoro-Leu at 50 and 67 Deposited 2003-05-13 | Different construct Different mutation/modification 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：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
pH 5.6；SEEDED FROM DROP CONTAINING CONTAINING 5 MUL 20MG/ML UBIQUITIN AND 5 MUL 30% PEG 4000 IN 50MM CACODYLATE-HCL PH 5.6. STORED IN 38% PEG 4000.
|
Resolution 1.32 Å |
| 2L3Z Proton-Detected 4D DREAM Solid-State NMR Structure of Ubiquitin Deposited 2010-09-27 | Different construct Different experimental method Different experimental conditions | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
Fragment：UNP Residues 1-76
|
Not recorded | No recorded non-water small molecule |
SOLID-STATE NMR
NMR measurement conditions
pH 4.1；298 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition
100 % [U-13C; U-15N; U-2H] Ubiquitin, 20% H2O, 80% D2O in crystallization buffer | 20% H2O, 80% D2O in crystallization buffer
|
Resolution not provided |
| 2LVO Structure of the gp78CUE domain bound to monubiquitin Deposited 2012-07-09 | Different construct Different oligomeric state Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.2；298 K；Pressure ambient
NMR sample composition
50 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2LVP gp78CUE domain bound to the distal ubiquitin of K48-linked diubiquitin Deposited 2012-07-09 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
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 7.2；298 K；Pressure ambient
NMR sample composition
50 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2LVQ gp78CUE domain bound to the proximal ubiquitin of K48-linked diubiquitin Deposited 2012-07-09 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
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 7.2；298 K；Pressure ambient
NMR sample composition
50 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2LZ6 Distinct ubiquitin binding modes exhibited by sh3 domains: molecular determinants and functional implications Deposited 2012-09-24 | Different construct Different oligomeric state Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition
0.2 mM [U-99% 15N] CD2AP SH3-C, 1 mM Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.25 mM [U-99% 15N] Ubiquitin, 1 mM CD2AP SH3-C, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.9 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 0.46 mM [U-99% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.828 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.37 mM [U-99% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.78 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.75 mM [U-99% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.25 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.75 mM [U-99% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2MBO K11-linked Diubiquitin average solution structure at pH 6.8, 0 mM NaCl Deposited 2013-08-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–76（76 aa）
Fragment：UNP residues 1-76
Chain B
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；296 K；Pressure ambient
NMR sample composition
75 uM [U-99% 15N] ubiquitin, 20 mM sodium phosphate, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 2MBQ K11-linked Diubiquitin average solution structure at pH 6.8, 150 mM NaCl Deposited 2013-08-03 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–76（76 aa）
Fragment：UNP residues 1-76
Chain B
1–76（76 aa）
Fragment：UNP 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) 150；Pressure ambient
NMR sample composition
75 uM [U-99% 15N] ubiquitin, 20 mM sodium phosphate, 150 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 2MCN Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications Deposited 2013-08-22 | Different construct Different oligomeric state Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition
0.2 mM [U-99% 15N] CD2AP SH3-A, 1 mM ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.25 mM [U-99% 15N] ubiquitin, mM CD2AP SH3-A, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.9 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 0.46 mM [U-99% 15N ubiquitin | 90% H2O/10% D2O
NMR sample composition
0.8 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 1.37 mM [U-99% 15N] ubiquitin | 90% H2O/10% D2O
NMR sample composition
0.7 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 1.75 mM [U-99% 15N] ubiquitin | 90% H2O/10% D2O
NMR sample composition
0.25 mM [U-99% 13C; U-99% 15N] CD2AP SH3-A, 1.75 MM [U-99% 15N] ubiquitin | 90% H2O/10% D2O
|
Resolution not provided |
| 2MI8 Solution structure of lysine-free (K0) ubiquitin Deposited 2013-12-09 | Different construct Different mutation/modification Different experimental conditions | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Mutation：K6R, K11R, K27R, K29R, K33R, K48R, K63R | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.2；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition
5 % [U-2H] D2O, 50 mM TRIS, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 2MJ5 Structure of the UBA Domain of Human NBR1 in Complex with Ubiquitin Deposited 2013-12-25 | Different construct Different oligomeric state Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–76（76 aa）
Fragment：UNP residuses 1-76
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.6；298 K；Pressure ambient
NMR sample composition
20 mM potassium phosphate-1, 5 mM potassium chloride-2, 1 mM EDTA-3, 1 mM benzamidine-4, 1 mM DTT-5, 0.02 % sodium azide-6, 1.2 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-7, 95 % H2O-8, 5 % D2O-9, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
20 mM potassium phosphate-10, 5 mM potassium chloride-11, 1 mM EDTA-12, 1 mM benzamidine-13, 1 mM DTT-14, 0.02 % sodium azide-15, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-16, 12.5 mg/mL Pf1 phage-17, 150 mM sodium chloride-18, 95 % H2O-19, 5 % D2O-20, 0.5 mM [U-100% 13C; U-100% 15N] NBR1_UBA-21, 2 mM Ubiquitin-22, 12.5 mg/mL Pf1 phage-23, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
20 mM potassium phosphate-24, 5 mM potassium chloride-25, 1 mM EDTA-26, 1 mM benzamidine-27, 1 mM DTT-28, 0.02 % sodium azide-29, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-30, 12.5 mg/mL Pf1 phage-31, 150 mM sodium chloride-32, 95 % H2O-33, 5 % D2O-34, 0.5 mM [U-100% 13C; U-100% 15N] NBR1_UBA-35, 2 mM Ubiquitin-36, 12.5 mg/mL Pf1 phage-37, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
2 mM NBR1_UBA-38, 0.5 mM [U-100% 13C; U-100% 15N] Ubiquitin-39, 12.5 mg/mL Pf1 phage-40, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
1 mM [U-100% 15N] NBR1_UBA-41, 4.5 mM Ubiquitin-42, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 2MOR A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings Deposited 2014-04-29 | Different construct Different experimental conditions | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
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 6.6；292 K；Pressure ambient
NMR measurement conditions
pH 6.6；298 K；Pressure ambient
NMR measurement conditions
pH 6.6；304 K；Pressure ambient
NMR sample composition
0.7 mM [U-13C; U-15N] Ubiquitin, 10 mM phosphate, 5 w/v DMPC:DHPC(3:1), 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 2MRE NMR structure of the Rad18-UBZ/ubiquitin complex Deposited 2014-07-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–76（76 aa）
Fragment：unp residues 1-76
|
Not recorded | ZN ZINC ION × 1 |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 125；Pressure ambient
NMR sample composition
0.5 mM [U-13C; U-15N] Ubiquitin-binding zinc finger (UBZ) domain from human Rad18, 5 mM Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
2 mM [U-13C; U-15N] Ubiquitin, 7-10 mM Ubiquitin-binding zinc finger (UBZ) domain from human Rad18, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2MWS Structure of the complex of ubiquitin and the ubiquitin-like (UBL) domain of Ddi1 Deposited 2014-11-23 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–76（76 aa）
Fragment：UNP residues 1-76
|
Mutation：T12(3X9) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；296 K；Ionic strength (raw mmCIF value) 0.002；Pressure ambient
NMR sample composition
250 uM chain A, 250 uM [U-100% 15N] chain B, 5 % D2O, 20 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2N2K Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand Deposited 2015-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–76（76 aa）
Chain B
1–71（71 aa）
|
Mutation：N25C, K48C | MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 2 |
SOLUTION NMR
NMR measurement conditions
pH 6；303 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition
0.5 mM [U-100% 15N] N25C_MTS protein-1, 10 % v/v [U-99% 2H] D2O-2, 100 mM sodium chloride-3, 10 mM sodium acetate-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.5 mM [U-100% 15N] K48C_MTS protein-5, 10 % v/v [U-99% 2H] D2O-6, 100 mM sodium chloride-7, 10 mM sodium acetate-8, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-100% 15N] N25C_MTS mixture protein-9, 10 % v/v [U-99% 2H] D2O-10, 100 mM sodium chloride-11, 10 mM sodium acetate-12, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-100% 15N] K48C_MTS mixture protein-13, 10 % v/v [U-99% 2H] D2O-14, 100 mM sodium chloride-15, 10 mM sodium acetate-16, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.5 mM [U-100% 15N] 15N_distal-14N_proximal-17, 10 % v/v [U-99% 2H] D2O-18, 100 mM sodium chloride-19, 10 mM sodium acetate-20, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.5 mM [U-100% 15N] 14N_distal-15N_proximal-21, 10 % v/v [U-99% 2H] D2O-22, 100 mM sodium chloride-23, 10 mM sodium acetate-24, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2RR9 The solution structure of the K63-Ub2:tUIMs complex Deposited 2010-06-16 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
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；310 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition
2.4 mM ubiquitin 1-1, 2.4 mM ubiquitin 2-2, 2.4 mM [U-13C; U-15N] tandem UIMs of Rap80-3, 1 mM DTT-4, 50 mM sodium phosphate-5, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
2 mM ubiquitin 1-6, 2 mM ubiquitin 2-7, 2 mM [U-13C; U-15N; U-70% 2H] tandem UIMs of Rap80-8, 1 mM DTT-9, 50 mM sodium phosphate-10, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
2.9 mM [U-13C; U-15N] ubiquitin 1-11, 2.9 mM ubiquitin 2-12, 2.9 mM tandem UIMs of Rap80-13, 1 mM DTT-14, 50 mM sodium phosphate-15, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
2.9 mM ubiquitin 1-16, 2.9 mM [U-13C; U-15N] ubiquitin 2-17, 2.9 mM tandem UIMs of Rap80-18, 1 mM DTT-19, 50 mM sodium phosphate-20, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2RSU Alternative structure of Ubiquitin Deposited 2012-06-15 | Different construct Different mutation/modification Different experimental conditions | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Mutation：Q41N | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.2；298 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition
0.5 mM [U-15N] protein-1, 20 mM [U-99% 2H] TRIS-2, 1 mM DSS-3, 250 mM sodium chloride-4, 6 mg/mL Pf1 bacteriopharge-5, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
2.0 mM [U-99% 13C; U-99% 15N] protein-6, 20 mM [U-99% 2H] TRIS-7, 1 mM DSS-8, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 2RU6 The pure alternative state of ubiquitin Deposited 2013-12-04 | Different construct Different mutation/modification Different experimental conditions | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Mutation：Q41N | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.2；298 K；Ionic strength (raw mmCIF value) 20；Pressure 250
NMR sample composition
20 mM [U-100% 2H] Tris(hydroxymethyl)aminomethane-1, 2 mM [U-100% 13C; U-100% 15N] ubiquitin-2, 0.2 mM DSS-3, 88% H2O/12% D2O | 88% H2O/12% D2O
|
Resolution not provided |
| 3ALB Cyclic Lys48-linked tetraubiquitin Deposited 2010-07-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
|
Not recorded | SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；289 K；20% PEG 3350, 0.2M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 1.85 Å R-free 0.239 |
| 3AUL Crystal structure of wild-type Lys48-linked diubiquitin in an open conformation Deposited 2011-02-09 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
77–152（76 aa）
Fragment：Ubiquitin
Chain B
77–152（76 aa）
Fragment：Ubiquitin
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20% PEG 3350, 0.2M litium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.39 Å R-free 0.252 |
| 3B08 Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin Deposited 2011-06-07 | Different construct Different oligomeric state 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
1–152（152 aa）
Fragment：linear di ubiquitin, UNP residues 1-152
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M tri-sodium citrate, 90mM HEPES-NaOH buffer, 100mM potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.211 |
| 3B08 Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin Deposited 2011-06-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–152（152 aa）
Fragment：linear di ubiquitin, UNP residues 1-152
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M tri-sodium citrate, 90mM HEPES-NaOH buffer, 100mM potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.211 |
| 3B08 Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin Deposited 2011-06-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
1–152（152 aa）
Fragment：linear di ubiquitin, UNP residues 1-152
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M tri-sodium citrate, 90mM HEPES-NaOH buffer, 100mM potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.211 |
| 3B08 Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin Deposited 2011-06-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain J
1–152（152 aa）
Fragment：linear di ubiquitin, UNP residues 1-152
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.3M tri-sodium citrate, 90mM HEPES-NaOH buffer, 100mM potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.211 |
| 3B0A Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin Deposited 2011-06-07 | Different construct Different oligomeric state 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
1–152（152 aa）
Fragment：linear di ubiquitin, UNP residues 1-152
|
Not recorded | TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.45M tri-ammonium citrate (pH 7.0), 3% 1,6-diaminohexane, VAPOR DIFFUSION, SITTING DROP, temperature 20K, temperature 293K
|
Resolution 1.90 Å R-free 0.227 |
| 3B0A Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin Deposited 2011-06-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–152（152 aa）
Fragment：linear di ubiquitin, UNP residues 1-152
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.45M tri-ammonium citrate (pH 7.0), 3% 1,6-diaminohexane, VAPOR DIFFUSION, SITTING DROP, temperature 20K, temperature 293K
|
Resolution 1.90 Å R-free 0.227 |
| 3OFI Crystal structure of human insulin-degrading enzyme in complex with ubiquitin Deposited 2010-08-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 DIO 1,4-DIETHYLENE DIOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；10-13% PEG MME 5000, 100 MM HEPES PH 7.0. 4-14% Tacsimate, 10% Dioxane, vapor diffusion, hanging drop, temperature 291K
|
Resolution 2.35 Å R-free 0.240 |
| 3OFI Crystal structure of human insulin-degrading enzyme in complex with ubiquitin Deposited 2010-08-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 | ZN ZINC ION × 1 DIO 1,4-DIETHYLENE DIOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；10-13% PEG MME 5000, 100 MM HEPES PH 7.0. 4-14% Tacsimate, 10% Dioxane, vapor diffusion, hanging drop, temperature 291K
|
Resolution 2.35 Å R-free 0.240 |
| 3Q3F Engineering Domain-Swapped Binding Interfaces by Mutually Exclusive Folding: Insertion of Ubiquitin into position 103 of Barnase Deposited 2010-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–76（75 aa）
Fragment：UNP P00648 48-150 and 151-157, UNP P0CG48 residues 2-76
|
Not recorded | SO4 SULFATE ION × 16 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10 mM Tris (pH 8.0), 1 M (NH4)2SO4, 1.5% isopropanol (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.17 Å R-free 0.233 |
| 3RUL New strategy to analyze structures of glycopeptide-target complexes Deposited 2011-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | TLA L(+)-TARTARIC ACID × 2 N1L 2-amino-2-deoxy-beta-D-glucopyranuronic acid × 1 MAN alpha-D-mannopyranose × 1 M12 10-METHYLUNDECANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG3350, 0.2M ammonium tartrate, 0.015M CYMAL-7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.277 |
| 3RUL New strategy to analyze structures of glycopeptide-target complexes Deposited 2011-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | TLA L(+)-TARTARIC ACID × 2 CL CHLORIDE ION × 1 N1L 2-amino-2-deoxy-beta-D-glucopyranuronic acid × 1 MAN alpha-D-mannopyranose × 1 M12 10-METHYLUNDECANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG3350, 0.2M ammonium tartrate, 0.015M CYMAL-7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.277 |
| 3RUL New strategy to analyze structures of glycopeptide-target complexes Deposited 2011-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | N1L 2-amino-2-deoxy-beta-D-glucopyranuronic acid × 1 MAN alpha-D-mannopyranose × 1 M12 10-METHYLUNDECANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG3350, 0.2M ammonium tartrate, 0.015M CYMAL-7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.277 |
| 3RUL New strategy to analyze structures of glycopeptide-target complexes Deposited 2011-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | N1L 2-amino-2-deoxy-beta-D-glucopyranuronic acid × 1 MAN alpha-D-mannopyranose × 1 M12 10-METHYLUNDECANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；24% PEG3350, 0.2M ammonium tartrate, 0.015M CYMAL-7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.277 |
| 3TMP The catalytic domain of human deubiquitinase DUBA in complex with ubiquitin aldehyde Deposited 2011-08-31 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–76（76 aa）
Fragment：Ubiquitin-like 1
|
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 5.8；293 K；20% PEG3350, 0.2 M Ammonium Fluoride, and 0.1M Bis-Tris, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.91 Å R-free 0.227 |
| 3TMP The catalytic domain of human deubiquitinase DUBA in complex with ubiquitin aldehyde Deposited 2011-08-31 | Different construct Different mutation/modification Different oligomeric state Different experimental method 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-like 1
|
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 5.8；293 K；20% PEG3350, 0.2 M Ammonium Fluoride, and 0.1M Bis-Tris, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.91 Å R-free 0.227 |
| 3TMP The catalytic domain of human deubiquitinase DUBA in complex with ubiquitin aldehyde Deposited 2011-08-31 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
1–76（76 aa）
Fragment：Ubiquitin-like 1
|
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 5.8；293 K；20% PEG3350, 0.2 M Ammonium Fluoride, and 0.1M Bis-Tris, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.91 Å R-free 0.227 |
| 3TMP The catalytic domain of human deubiquitinase DUBA in complex with ubiquitin aldehyde Deposited 2011-08-31 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
1–76（76 aa）
Fragment：Ubiquitin-like 1
|
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 5.8；293 K；20% PEG3350, 0.2 M Ammonium Fluoride, and 0.1M Bis-Tris, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.91 Å R-free 0.227 |
| 3U30 Crystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin Deposited 2011-10-04 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
18–169（152 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；18% isopropanol, 0.09 M MES, 19.8% PEG 2K MME, 10 mM sodium bromide., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.43 Å R-free 0.258 |
| 3U30 Crystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin Deposited 2011-10-04 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
18–169（152 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；18% isopropanol, 0.09 M MES, 19.8% PEG 2K MME, 10 mM sodium bromide., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.43 Å R-free 0.258 |
| 3UGB UbcH5c~Ubiquitin Conjugate Deposited 2011-11-02 | 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 B
1–76（76 aa）
Fragment：unp residues 1-76
|
Not recorded | GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M tri-potassium citrate, 20% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.35 Å R-free 0.252 |
| 3V6C Crystal Structure of USP2 in complex with mutated ubiquitin Deposited 2011-12-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
74–150（77 aa）
|
Mutation：G76S, K82N, K87T, T88H | CL CHLORIDE ION × 2 GOL GLYCEROL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；21% PEG 3350,0.2 M CaCl,
0.1 Bis-Tris pH 7.0,
glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.220 |
| 3V6E Crystal Structure of USP2 and a mutant form of Ubiquitin Deposited 2011-12-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
74–150（77 aa）
|
Mutation：G76S, K82N, T85S, T88H | ZN ZINC ION × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；21% PEG3350, 0.2 M Calcium Chloride,0.1 Bis-Tris pH 7.0,
glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.234 |
| 3VFK The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier Deposited 2012-01-09 | 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 × 2 PDB declaration: dimeric |
Chain A
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GCS 2-amino-2-deoxy-beta-D-glucopyranose × 1 T55 8-METHYLNONANOIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.1 M magnesium chloride, 0.1 M sodium acetate 4.6, 18% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.80 Å R-free 0.306 |
| 3VUW Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I Deposited 2012-07-09 | Different construct Different oligomeric state 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：Ubiquitin
|
Not recorded | ZN ZINC ION × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, pH 8.0, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.95 Å R-free 0.222 |
| 3VUW Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I Deposited 2012-07-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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
|
Not recorded | ZN ZINC ION × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, pH 8.0, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.95 Å R-free 0.222 |
| 3VUW Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I Deposited 2012-07-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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
|
Not recorded | ZN ZINC ION × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, pH 8.0, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.95 Å R-free 0.222 |
| 3VUX Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II Deposited 2012-07-09 | Different construct Different oligomeric state 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：Ubiquitin
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.203 |
| 3VUX Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II Deposited 2012-07-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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
|
Not recorded | ZN ZINC ION × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.203 |
| 3VUX Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II Deposited 2012-07-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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
|
Not recorded | ZN ZINC ION × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.203 |
| 3VUY Crystal structure of A20 ZF7 in complex with linear tetraubiquitin Deposited 2012-07-09 | Different construct Different oligomeric state 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：Ubiquitin
|
Not recorded | ZN ZINC ION × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 8% PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.98 Å R-free 0.255 |
| 3VUY Crystal structure of A20 ZF7 in complex with linear tetraubiquitin Deposited 2012-07-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–76（76 aa）
Fragment：Ubiquitin
|
Not recorded | ZN ZINC ION × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 8% PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.98 Å R-free 0.255 |
| 3VUY Crystal structure of A20 ZF7 in complex with linear tetraubiquitin Deposited 2012-07-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–76（76 aa）
Fragment：Ubiquitin
|
Not recorded | ZN ZINC ION × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 8% PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.98 Å R-free 0.255 |
| 3WXE Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin Deposited 2014-07-30 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–148（148 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；50mM Tris-HCl buffer, 9% PEG4000, 100mM magnesium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.50 Å R-free 0.247 |
| 3WXF Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin Deposited 2014-07-30 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–148（148 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl buffer, 23% PEG3350, 0.2M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.229 |
| 3WXF Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin Deposited 2014-07-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–148（148 aa）
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl buffer, 23% PEG3350, 0.2M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.229 |
| 3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 | 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
77–152（76 aa）
Fragment：RESIDUES 77-152
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
|
Resolution 2.21 Å R-free 0.211 |
| 3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain H
77–152（76 aa）
Fragment：RESIDUES 77-152
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
|
Resolution 2.21 Å R-free 0.211 |
| 3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain L
77–152（76 aa）
Fragment：RESIDUES 77-152
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
|
Resolution 2.21 Å R-free 0.211 |
| 3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
77–152（76 aa）
Fragment：RESIDUES 77-152
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
|
Resolution 2.21 Å R-free 0.211 |
| 4AUQ Structure of BIRC7-UbcH5b-Ub complex. Deposited 2012-05-21 | 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 × 6 PDB declaration: hexameric |
Chain C
1–76（76 aa）
Fragment：UBIQUITIN, RESIDUES 1-76
Chain F
1–76（76 aa）
Fragment：UBIQUITIN, RESIDUES 1-76
|
Not recorded | ZN ZINC ION × 4 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.18 Å R-free 0.249 |
| 4BOS Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide Deposited 2013-05-22 | 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 × 5 PDB declaration: pentameric |
Chain C
1–76（76 aa）
Fragment：RESIDUES 1-76
Chain E
1–76（76 aa）
Fragment：RESIDUES 1-76
|
Not recorded | NO3 NITRATE ION × 5 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
21% PEG 3,350, 100 MM SODIUM ACETATE, 200 MM MAGNESIUM NITRATE, PH 5.6
|
Resolution 2.35 Å R-free 0.238 |
| 4BOZ Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin Deposited 2013-05-22 | Different construct Different oligomeric state 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
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.15 M POTASSIUM THIOCYANATE, 18% PEG 5K MME, 0.1 M SODIUM ACETATE PH 5.5
|
Resolution 3.03 Å R-free 0.254 |
| 4BOZ Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin Deposited 2013-05-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.15 M POTASSIUM THIOCYANATE, 18% PEG 5K MME, 0.1 M SODIUM ACETATE PH 5.5
|
Resolution 3.03 Å R-free 0.254 |
| 4BOZ Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin Deposited 2013-05-22 | Different construct Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.15 M POTASSIUM THIOCYANATE, 18% PEG 5K MME, 0.1 M SODIUM ACETATE PH 5.5
|
Resolution 3.03 Å R-free 0.254 |
| 4BVU Structure of Shigella effector OspG in complex with host UbcH5c- Ubiquitin conjugate Deposited 2013-06-28 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；0.1 M TRIS PH 8.5, 20% ETOH
|
Resolution 2.70 Å R-free 0.291 |
| 4DDG Crystal structure of human OTUB1/UbcH5b~Ub/Ub Deposited 2012-01-18 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain D
1–76（76 aa）
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）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG1500, 0.1 M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 3.30 Å R-free 0.280 |
| 4DDG Crystal structure of human OTUB1/UbcH5b~Ub/Ub Deposited 2012-01-18 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain M
1–76（76 aa）
Chain N
1–76（76 aa）
Chain O
1–76（76 aa）
Chain P
1–76（76 aa）
Chain Q
1–76（76 aa）
Chain R
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG1500, 0.1 M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 3.30 Å R-free 0.280 |
| 4DDI Crystal structure of human OTUB1/UbcH5b~Ub/Ub Deposited 2012-01-18 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain D
1–76（76 aa）
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）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；293 K；25% PEG1500, 0.1 M SPG, pH 8.0, VAPOR DIFFUSION, temperature 293K
|
Resolution 3.80 Å R-free 0.273 |
| 4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
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 6.5；293 K；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.35 Å R-free 0.237 |
| 4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
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
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.35 Å R-free 0.237 |
| 4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27 | Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.35 Å R-free 0.237 |
| 4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
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 6.5；293 K；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.35 Å R-free 0.237 |
| 4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain M
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 6.5；293 K；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.35 Å R-free 0.237 |
| 4DHJ The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex Deposited 2012-01-27 | Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain H
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG350, 0.26-0.30 M sodium chloride, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.35 Å R-free 0.237 |
| 4DHZ The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub Deposited 2012-01-30 | Different construct Different mutation/modification Different oligomeric state 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）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；21% PEG10000, 0.1 M sodium chloride, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.11 Å R-free 0.288 |
| 4DHZ The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub Deposited 2012-01-30 | Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；21% PEG10000, 0.1 M sodium chloride, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.11 Å R-free 0.288 |
| 4FJV Crystal Structure of Human Otubain2 and Ubiquitin Complex Deposited 2012-06-12 | Different construct Different oligomeric state 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
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 3 NEH ETHANAMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；279 K；15 % (w/v) Polyethylene Glycol 3350, 0.1 M Magnesium Formate
, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 279K
|
Resolution 2.05 Å R-free 0.267 |
| 4FJV Crystal Structure of Human Otubain2 and Ubiquitin Complex Deposited 2012-06-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 NEH ETHANAMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；279 K；15 % (w/v) Polyethylene Glycol 3350, 0.1 M Magnesium Formate
, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 279K
|
Resolution 2.05 Å R-free 0.267 |
| 4FJV Crystal Structure of Human Otubain2 and Ubiquitin Complex Deposited 2012-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–76（76 aa）
Chain D
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 6 NEH ETHANAMINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；279 K；15 % (w/v) Polyethylene Glycol 3350, 0.1 M Magnesium Formate
, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 279K
|
Resolution 2.05 Å R-free 0.267 |
| 4HK2 U7Ub25.2540 Deposited 2012-10-14 | Different construct Different mutation/modification 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
75–150（76 aa）
|
Mutation：T7F, L8R, I13Y, R42W, Q49R, L69G, L71R | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；2.4 M AmSO4 and 0.1M Citric acid pH 4.0, vapor diffusion, hanging drop, temperature 277K
|
Resolution 1.40 Å R-free 0.236 |
| 4HK2 U7Ub25.2540 Deposited 2012-10-14 | Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
75–150（76 aa）
|
Mutation：T7F, L8R, I13Y, R42W, Q49R, L69G, L71R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；2.4 M AmSO4 and 0.1M Citric acid pH 4.0, vapor diffusion, hanging drop, temperature 277K
|
Resolution 1.40 Å R-free 0.236 |
| 4HK2 U7Ub25.2540 Deposited 2012-10-14 | Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
75–150（76 aa）
|
Mutation：T7F, L8R, I13Y, R42W, Q49R, L69G, L71R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；2.4 M AmSO4 and 0.1M Citric acid pH 4.0, vapor diffusion, hanging drop, temperature 277K
|
Resolution 1.40 Å R-free 0.236 |
| 4HK2 U7Ub25.2540 Deposited 2012-10-14 | Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
75–150（76 aa）
|
Mutation：T7F, L8R, I13Y, R42W, Q49R, L69G, L71R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；2.4 M AmSO4 and 0.1M Citric acid pH 4.0, vapor diffusion, hanging drop, temperature 277K
|
Resolution 1.40 Å R-free 0.236 |
| 4HXD Diversity of ubiquitin and ISG15 specificity amongst nairoviruses viral ovarian tumor domain proteases Deposited 2012-11-09 | Different construct Different oligomeric state 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
1–75（75 aa）
|
Not recorded | 4LJ 1.7.6 3-bromanylpropan-1-amine × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.25 M LiSO4, 0.10 M Bis-Tris, 29% PEG 3350, 40% (v/v) 1,3-butanediol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.85 Å R-free 0.278 |
| 4HXD Diversity of ubiquitin and ISG15 specificity amongst nairoviruses viral ovarian tumor domain proteases Deposited 2012-11-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–75（75 aa）
|
Not recorded | 4LJ 1.7.6 3-bromanylpropan-1-amine × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.25 M LiSO4, 0.10 M Bis-Tris, 29% PEG 3350, 40% (v/v) 1,3-butanediol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.85 Å R-free 0.278 |
| 4I6L Crystal structure of OTUB1 in complex with ubiquitin variant Deposited 2012-11-29 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
77–150（74 aa）
Fragment：UNP residues 77-150
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, and 20% (w/v) PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.49 Å R-free 0.266 |
| 4I6N Crystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin vinyl methyl ester Deposited 2012-11-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 NA SODIUM ION × 1 GVE METHYL 4-AMINOBUTANOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；3M ammonium sulfate, 0.1M bicine, 2mM L-glutathione, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 1.70 Å R-free 0.211 |
| 4I6N Crystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin vinyl methyl ester Deposited 2012-11-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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) | GVE METHYL 4-AMINOBUTANOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；3M ammonium sulfate, 0.1M bicine, 2mM L-glutathione, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 1.70 Å R-free 0.211 |
| 4IG7 Crystal structure of Trichinella spiralis UCH37 bound to Ubiquitin vinyl methyl ester Deposited 2012-12-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–75（75 aa）
|
Not recorded | GVE METHYL 4-AMINOBUTANOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；0.2 M ammonium chloride, 18% PEG3350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.239 |
| 4IUM Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin Deposited 2013-01-21 | 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 × 2 PDB declaration: dimeric |
Chain B
1–75（75 aa）
Fragment：UNP residues 1-75
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；100 mM MES, pH 6.2, 18% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.45 Å R-free 0.178 |
| 4JQW Crystal Structure of a Complex of NOD1 CARD and Ubiquitin Deposited 2013-03-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 | PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.6；291 K；100mM PCB, 25% PEG1500, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.90 Å R-free 0.270 |
| 4K1R Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain and Ubiquitin Deposited 2013-04-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
75–152（78 aa）
|
Not recorded | ZN ZINC ION × 3 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 3；293 K；0.02M Zinc chloride, 20% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.63 Å R-free 0.215 |
| 4K1R Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain and Ubiquitin Deposited 2013-04-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
75–152（78 aa）
|
Not recorded | ZN ZINC ION × 3 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 3；293 K；0.02M Zinc chloride, 20% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.63 Å R-free 0.215 |
| 4K1R Crystal structure of Schizosaccharomyces pombe sst2 catalytic domain and Ubiquitin Deposited 2013-04-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 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 × 6 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 3；293 K；0.02M Zinc chloride, 20% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.63 Å R-free 0.215 |
| 4K7S Crystal structure of Zn2-hUb (human ubiquitin) adduct from a solution 35 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 | Different construct 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 1-73
|
Not recorded | ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 35 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.271 |
| 4K7S Crystal structure of Zn2-hUb (human ubiquitin) adduct from a solution 35 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 | Different construct Different ligand/ion Different experimental method 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 1-73
|
Not recorded | ZN ZINC ION × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 35 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.271 |
| 4K7S Crystal structure of Zn2-hUb (human ubiquitin) adduct from a solution 35 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 | Different construct Different ligand/ion Different experimental method 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 1-73
|
Not recorded | ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 35 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.271 |
| 4K7U Crystal structure of Zn2.3-hUb (human ubiquitin) adduct from a solution 70 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 | Different construct 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
|
Not recorded | ZN ZINC ION × 4 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 70 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.196 |
| 4K7U Crystal structure of Zn2.3-hUb (human ubiquitin) adduct from a solution 70 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 | Different construct Different ligand/ion Different experimental method 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
|
Not recorded | ZN ZINC ION × 3 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 70 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.196 |
| 4K7U Crystal structure of Zn2.3-hUb (human ubiquitin) adduct from a solution 70 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 | Different construct Different ligand/ion Different experimental method 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
|
Not recorded | ZN ZINC ION × 2 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 70 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.196 |
| 4K7W Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 100 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 | Different construct 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
|
Not recorded | ZN ZINC ION × 4 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 100 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.267 |
| 4K7W Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 100 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 | Different construct Different ligand/ion Different experimental method 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
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 100 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.267 |
| 4K7W Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 100 mM zinc acetate/1.3 mM hUb Deposited 2013-04-17 | Different construct Different ligand/ion Different experimental method 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
|
Not recorded | ZN ZINC ION × 3 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 100 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.267 |
| 4KSK Gumby/Fam105B in complex with ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
76–152（77 aa）
Fragment：unp residues 76-152
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM Bis Tris, 200 mM AmSO4, 20% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.40 Å R-free 0.268 |
| 4KSK Gumby/Fam105B in complex with ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
76–152（77 aa）
Fragment：unp residues 76-152
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM Bis Tris, 200 mM AmSO4, 20% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.40 Å R-free 0.268 |
| 4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
76–228（153 aa）
Fragment：linear diubiquitin (unp residues 76-228)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.254 |
| 4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain T
76–228（153 aa）
Fragment：linear diubiquitin (unp residues 76-228)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.254 |
| 4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain V
76–228（153 aa）
Fragment：linear diubiquitin (unp residues 76-228)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.254 |
| 4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain X
76–228（153 aa）
Fragment：linear diubiquitin (unp residues 76-228)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.254 |
| 4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
76–228（153 aa）
Fragment：linear diubiquitin (unp residues 76-228)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.254 |
| 4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
76–228（153 aa）
Fragment：linear diubiquitin (unp residues 76-228)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.254 |
| 4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
76–228（153 aa）
Fragment：linear diubiquitin (unp residues 76-228)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.254 |
| 4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain J
76–228（153 aa）
Fragment：linear diubiquitin (unp residues 76-228)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.254 |
| 4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain L
76–228（153 aa）
Fragment：linear diubiquitin (unp residues 76-228)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.254 |
| 4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain N
76–228（153 aa）
Fragment：linear diubiquitin (unp residues 76-228)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.254 |
| 4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
76–228（153 aa）
Fragment：linear diubiquitin (unp residues 76-228)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.254 |
| 4KSL Gumby/Fam105B in complex with linear di-ubiquitin Deposited 2013-05-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain R
76–228（153 aa）
Fragment：linear diubiquitin (unp residues 76-228)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；298 K；100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.83 Å R-free 0.254 |
| 4LCD Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3 Deposited 2013-06-21 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
1–75（75 aa）
Fragment：UNP residues 1-75
|
Mutation：G75C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.2；298 K；0.1M Bis Tris Propane, 21% w/v PEG3350, 1% w/v polypropylene glycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.10 Å R-free 0.299 |
| 4LCD Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3 Deposited 2013-06-21 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
1–75（75 aa）
Fragment：UNP residues 1-75
|
Mutation：G75C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.2；298 K；0.1M Bis Tris Propane, 21% w/v PEG3350, 1% w/v polypropylene glycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.10 Å R-free 0.299 |
| 4LDT The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub Deposited 2013-06-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–76（76 aa）
Chain D
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 4 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；1:1 mix of 12 mg/mL purified complex and well solution (100 mM Bis-Tris, pH 6.0, 200 mM magnesium chloride, 22% PEG3350), crystals appeared in about 2 to 3 days, cryoprotection with well solution + 10% ethylene glycol, flash frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
|
Resolution 1.90 Å R-free 0.223 |
| 4MDK Cdc34-ubiquitin-CC0651 complex Deposited 2013-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
76–152（77 aa）
Fragment：UNP residues 76-152
|
Not recorded | U94 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；28% PEG3350, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.61 Å R-free 0.259 |
| 4MDK Cdc34-ubiquitin-CC0651 complex Deposited 2013-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
76–152（77 aa）
Fragment：UNP residues 76-152
|
Not recorded | U94 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；28% PEG3350, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.61 Å R-free 0.259 |
| 4MDK Cdc34-ubiquitin-CC0651 complex Deposited 2013-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
76–152（77 aa）
Fragment：UNP residues 76-152
|
Not recorded | U94 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；28% PEG3350, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.61 Å R-free 0.259 |
| 4MDK Cdc34-ubiquitin-CC0651 complex Deposited 2013-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
76–152（77 aa）
Fragment：UNP residues 76-152
|
Not recorded | U94 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；28% PEG3350, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.61 Å R-free 0.259 |
| 4MM3 Crystal structure of SARS-CoV papain-like protease PLpro in complex with ubiquitin aldehyde Deposited 2013-09-08 | 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 × 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) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M HEPES, pH 7.5, 10% isopropanol, 20% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.75 Å R-free 0.279 |
| 4MSM Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant bound to ubiquitin Deposited 2013-09-18 | Different construct Different oligomeric state 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
77–152（76 aa）
Fragment：UNP residues 77-152
|
Not recorded | ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2M Ammonium Phosphate dibasic, 20%w/v PEG 3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.74 Å R-free 0.225 |
| 4MSM Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant bound to ubiquitin Deposited 2013-09-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 × 6 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2M Ammonium Phosphate dibasic, 20%w/v PEG 3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.74 Å R-free 0.225 |
| 4MSQ Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 catalytic domain bound to ubiquitin Deposited 2013-09-18 | Different construct Different oligomeric state 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
77–152（76 aa）
Fragment：UNP residues 77-152
|
Not recorded | ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.3；293 K；0.2 M Sodium citrate tribasic dihydrate, 20% w/v PEG 3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.95 Å R-free 0.207 |
| 4MSQ Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 catalytic domain bound to ubiquitin Deposited 2013-09-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 × 6 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.3；293 K；0.2 M Sodium citrate tribasic dihydrate, 20% w/v PEG 3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.95 Å R-free 0.207 |
| 4NQK Structure of an Ubiquitin complex Deposited 2013-11-25 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain E
76–152（77 aa）
Fragment：UNP residues 76-152
Chain F
76–152（77 aa）
Fragment：UNP residues 76-152
Chain G
76–152（77 aa）
Fragment：UNP residues 76-152
Chain H
76–152（77 aa）
Fragment：UNP residues 76-152
Chain I
76–152（77 aa）
Fragment：UNP residues 76-152
Chain J
76–152（77 aa）
Fragment：UNP residues 76-152
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；22% PEG3350, 0.2 M Tri-Li Citrate, 3% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.70 Å R-free 0.285 |
| 4UN2 Crystal structure of the UBA domain of Dsk2 in complex with Ubiquitin Deposited 2014-05-23 | Different construct Different oligomeric state 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 | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH 8.5, 20% PEG 8000
|
Resolution 1.51 Å R-free 0.196 |
| 4V3K RNF38-UbcH5B-UB complex Deposited 2014-10-20 | 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 E
77–152（76 aa）
Fragment：RESIDUES 77-152
|
Not recorded | CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
50 MM TRIS-HCL, PH 8.5 AND 2.3 M AMMONIUM SULFATE
|
Resolution 2.04 Å R-free 0.223 |
| 4V3K RNF38-UbcH5B-UB complex Deposited 2014-10-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
77–152（76 aa）
Fragment：RESIDUES 77-152
|
Not recorded | CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
50 MM TRIS-HCL, PH 8.5 AND 2.3 M AMMONIUM SULFATE
|
Resolution 2.04 Å R-free 0.223 |
| 4V3L RNF38-UB-UbcH5B-Ub complex Deposited 2014-10-20 | 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
77–152（76 aa）
Fragment：RESIDUES 77-152
Chain D
77–152（76 aa）
Fragment：RESIDUES 77-152
|
Not recorded | EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
50 MM HEPES, PH 7.5, 0.2 M MAGNESIUM ACETATE AND 13% (W/V) PEG 8K
|
Resolution 1.53 Å R-free 0.193 |
| 4XOK Observing the overall rocking motion of a protein in a crystal. Deposited 2015-01-16 | Different construct 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）
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20mg/ml Ubi in 20mM NH4Ac pH4.3, 50mM HEPES pH7.0,
35% PEG 1500, 25mM Zn Acetate
|
Resolution 2.20 Å R-free 0.324 |
| 4XOK Observing the overall rocking motion of a protein in a crystal. Deposited 2015-01-16 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20mg/ml Ubi in 20mM NH4Ac pH4.3, 50mM HEPES pH7.0,
35% PEG 1500, 25mM Zn Acetate
|
Resolution 2.20 Å R-free 0.324 |
| 4XOK Observing the overall rocking motion of a protein in a crystal. Deposited 2015-01-16 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20mg/ml Ubi in 20mM NH4Ac pH4.3, 50mM HEPES pH7.0,
35% PEG 1500, 25mM Zn Acetate
|
Resolution 2.20 Å R-free 0.324 |
| 4XOL Observing the overall rocking motion of a protein in a crystal - Cubic Ubiquitin crystals. Deposited 2015-01-16 | Different construct 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）
|
Not recorded | ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.33；293 K；100mM MES pH 6.33, 20% PEG 3350, 100mM Zn Acetate.
|
Resolution 2.91 Å R-free 0.269 |
| 4XOL Observing the overall rocking motion of a protein in a crystal - Cubic Ubiquitin crystals. Deposited 2015-01-16 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.33；293 K；100mM MES pH 6.33, 20% PEG 3350, 100mM Zn Acetate.
|
Resolution 2.91 Å R-free 0.269 |
| 4ZQS New compact conformation of linear Ub2 structure Deposited 2015-05-11 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–152（152 aa）
Chain B
1–152（152 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；0.1M Tris-HCl pH 8.0, 0.1M magnesium acetate, 20% PEG 3350, 20% PEG 400
|
Resolution 1.80 Å R-free 0.232 |
| 5A5B Structure of the 26S proteasome-Ubp6 complex Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric |
Chain 9
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM vitrification conditions
Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- HOMEMADE PLUNGER,
|
Resolution 9.50 Å |
| 5AIU A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink) Deposited 2015-02-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
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 EDO 1,2-ETHANEDIOL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
1,2-ETHANEDIOL
|
Resolution 2.21 Å R-free 0.255 |
| 5B83 Crystal structure of Optineurin UBAN in complex with linear ubiquitin Deposited 2016-06-12 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–304（304 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；16% PEG 3350, 250mM Potassium formate
|
Resolution 2.69 Å R-free 0.254 |
| 5B83 Crystal structure of Optineurin UBAN in complex with linear ubiquitin Deposited 2016-06-12 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
1–304（304 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；16% PEG 3350, 250mM Potassium formate
|
Resolution 2.69 Å R-free 0.254 |
| 5C7J CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT Deposited 2015-06-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–74（74 aa）
Fragment：UNP residues 1-74
|
Mutation：T9A, K11W, T12G, Q62R, K63Y, E64D, T66Q, L71G | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；The NEDD4 and Ubiquitin Variant was mixed at molar ratio ~1:2, and then concentrated to 15mg/ml.
The protein sample was mixed with Trypsin at a 1:1000 (W/W) Trypsin:protein ratio before setting up crystallization.
Crystal was initially obtained from Molecular Dimentions Proplex screen condition E04.
Crystal used for structure refinement was grown in 20% PEG8000, 10% Glycerol, 0.1M HEPES pH 7.0 in hanging drop setup, using 1.5uL protein, 1.5uL well solution over 0.5 mL reservoir buffer at 20 C.
Crystals grow to mountable size in 4 days. Harvested crystal was flash-frozen in liquid nitrogen. 20% Glycerol was used as the cryo-protectant
|
Resolution 3.00 Å R-free 0.277 |
| 5C7J CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT Deposited 2015-06-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–74（74 aa）
Fragment：UNP residues 1-74
|
Mutation：T9A, K11W, T12G, Q62R, K63Y, E64D, T66Q, L71G | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；The NEDD4 and Ubiquitin Variant was mixed at molar ratio ~1:2, and then concentrated to 15mg/ml.
The protein sample was mixed with Trypsin at a 1:1000 (W/W) Trypsin:protein ratio before setting up crystallization.
Crystal was initially obtained from Molecular Dimentions Proplex screen condition E04.
Crystal used for structure refinement was grown in 20% PEG8000, 10% Glycerol, 0.1M HEPES pH 7.0 in hanging drop setup, using 1.5uL protein, 1.5uL well solution over 0.5 mL reservoir buffer at 20 C.
Crystals grow to mountable size in 4 days. Harvested crystal was flash-frozen in liquid nitrogen. 20% Glycerol was used as the cryo-protectant
|
Resolution 3.00 Å R-free 0.277 |
| 5C7M CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT Deposited 2015-06-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–75（75 aa）
Fragment：UNP residues 1-75
|
Mutation：Q2H, F3L, T9R, I44L, A46G, K48N, Q49K, T66N, H68Y, V70L, L73R, R74L | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；The ITCH and ubiquitin variant ubv.it.02 were mixed at molarity ratio 1:2, and then concentrated to 17mg/ml.
The protein sample was mixed with 1mg/mL chymotrypsin at a 1:1000 (W/W) chymotrypsin:protein ratio right before set up crystallization. Crystal was initially obtained from SGC-I screen condition A05. Crystal used for structure refinement was grown in 1.6M NH4SO4, 0.2M NaAc, 0.1M HEPES pH 7.5, 5% Ethylene Glycol in hanging drop setup, using 1.2uL protein, 1.2uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size for ~1 weeks. Harvested crystal was flash-frozen in liquid nitrogen. A well solution containing 20% glycerol was used as the cryo-protectant
|
Resolution 3.03 Å R-free 0.297 |
| 5C7M CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT Deposited 2015-06-24 | Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–75（75 aa）
Fragment：UNP residues 1-75
|
Mutation：Q2H, F3L, T9R, I44L, A46G, K48N, Q49K, T66N, H68Y, V70L, L73R, R74L | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；The ITCH and ubiquitin variant ubv.it.02 were mixed at molarity ratio 1:2, and then concentrated to 17mg/ml.
The protein sample was mixed with 1mg/mL chymotrypsin at a 1:1000 (W/W) chymotrypsin:protein ratio right before set up crystallization. Crystal was initially obtained from SGC-I screen condition A05. Crystal used for structure refinement was grown in 1.6M NH4SO4, 0.2M NaAc, 0.1M HEPES pH 7.5, 5% Ethylene Glycol in hanging drop setup, using 1.2uL protein, 1.2uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size for ~1 weeks. Harvested crystal was flash-frozen in liquid nitrogen. A well solution containing 20% glycerol was used as the cryo-protectant
|
Resolution 3.03 Å R-free 0.297 |
| 5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–75（75 aa）
|
Mutation：K48LYQ, G76AYE Non-standard monomer：Yes (specific site not provided by mmCIF) | 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 construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
1–75（75 aa）
|
Mutation：K48LYQ, G76AYE 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 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
|
Resolution 2.85 Å R-free 0.264 |
| 5H07 TNIP2-Ub complex, C2 form Deposited 2016-10-04 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–228（228 aa）
Fragment：UNP residues 1-228
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；ammonium acetate, PEG3350, Tris-HCl
|
Resolution 2.59 Å R-free 0.273 |
| 5NL4 Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 | Different construct Different mutation/modification 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：E16V | ZN ZINC ION × 2 ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 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, 35 mM Zn(CH3COO)2
|
Resolution 1.32 Å R-free 0.213 |
| 5NL4 Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 | Different construct Different mutation/modification Different ligand/ion Different experimental method 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 ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 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, 35 mM Zn(CH3COO)2
|
Resolution 1.32 Å R-free 0.213 |
| 5NL4 Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 | Different construct Different mutation/modification Different ligand/ion Different experimental method 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 PEG DI(HYDROXYETHYL)ETHER × 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, 35 mM Zn(CH3COO)2
|
Resolution 1.32 Å R-free 0.213 |
| 5NLF Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 | Different construct Different mutation/modification 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：E16V | ZN ZINC ION × 6 ACT ACETATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 100 mM Zn(CH3COO)2
|
Resolution 1.50 Å R-free 0.180 |
| 5NLF Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 | Different construct Different mutation/modification Different ligand/ion Different experimental method 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 × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 100 mM Zn(CH3COO)2
|
Resolution 1.50 Å R-free 0.180 |
| 5NLF Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 | Different construct Different mutation/modification Different ligand/ion Different experimental method 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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 100 mM Zn(CH3COO)2
|
Resolution 1.50 Å R-free 0.180 |
| 5NLI Crystal structure of Zn2-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/10% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 | Different construct Different mutation/modification 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：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, 35 mM Zn(CH3COO)2 and 10% v/v TFE
|
Resolution 1.53 Å R-free 0.202 |
| 5NLI Crystal structure of Zn2-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/10% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 | Different construct Different mutation/modification Different ligand/ion Different experimental method 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 × 1 EDO 1,2-ETHANEDIOL × 2 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, 35 mM Zn(CH3COO)2 and 10% v/v TFE
|
Resolution 1.53 Å R-free 0.202 |
| 5NLI Crystal structure of Zn2-E16V human ubiquitin (hUb) mutant adduct, from a solution 35 mM zinc acetate/10% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 | Different construct Different mutation/modification Different ligand/ion Different experimental method 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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 35 mM Zn(CH3COO)2 and 10% v/v TFE
|
Resolution 1.53 Å R-free 0.202 |
| 5NMC Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM hUb Deposited 2017-04-05 | Different construct 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）
|
Not recorded | ACT ACETATE ION × 2 ZN ZINC ION × 4 |
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 and 20% v/v TFE
|
Resolution 1.70 Å R-free 0.276 |
| 5NMC Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM hUb Deposited 2017-04-05 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | ACT ACETATE ION × 2 ZN ZINC ION × 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 and 20% v/v TFE
|
Resolution 1.70 Å R-free 0.276 |
| 5NMC Crystal structure of Zn3-hUb(human ubiquitin) adduct from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM hUb Deposited 2017-04-05 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–76（76 aa）
|
Not recorded | ACT ACETATE ION × 1 ZN ZINC ION × 3 |
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 and 20% v/v TFE
|
Resolution 1.70 Å R-free 0.276 |
| 5OE7 Structure of OTULIN bound to the Met1-linked diubiquitin activity probe Deposited 2017-07-07 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–146（146 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；298 K；1.9-2.1 M Ammonium sulphate, 100 mM bis-tris
|
Resolution 2.95 Å R-free 0.309 |
| 5OHM K33-specific affimer bound to K33 diUb Deposited 2017-07-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
609–684（76 aa）
Chain C
609–684（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；20% PEG3350
0.2M potassium thiocyanate
|
Resolution 3.80 Å R-free 0.282 |
| 5OHM K33-specific affimer bound to K33 diUb Deposited 2017-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
609–684（76 aa）
Chain G
609–684（76 aa）
|
Not recorded | 15P POLYETHYLENE GLYCOL (N=34) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；20% PEG3350
0.2M potassium thiocyanate
|
Resolution 3.80 Å R-free 0.282 |
| 5OHM K33-specific affimer bound to K33 diUb Deposited 2017-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain I
609–684（76 aa）
Chain K
609–684（76 aa）
|
Not recorded | 15P POLYETHYLENE GLYCOL (N=34) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；20% PEG3350
0.2M potassium thiocyanate
|
Resolution 3.80 Å R-free 0.282 |
| 5OHV K33-specific affimer bound to K33 diUb Deposited 2017-07-18 | 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 × 4 PDB declaration: tetrameric |
Chain A
1–76（76 aa）
Chain C
1–76（76 aa）
|
Not recorded | SO4 SULFATE ION × 2 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.2；295 K；21% PEG 3350
200 mM Li2SO4
100 mM NaOAc pH 5.2
|
Resolution 2.80 Å R-free 0.224 |
| 5OXH C-terminally retracted ubiquitin T66V/L67N mutant Deposited 2017-09-06 | Different construct Different mutation/modification 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：T66V, L67N Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；3.2 M ammonium sulfate, 0.1 M bicine (pH 9.0); 1:1 protein to reservoir ratio
|
Resolution 1.60 Å R-free 0.223 |
| 5OXI C-terminally retracted ubiquitin L67S mutant Deposited 2017-09-06 | Different construct Different mutation/modification 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：L67S | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；3 M ammonium sulfate, 0.1 M MES (pH 6.0); 2:1 protein to reservoir ratio
|
Resolution 1.63 Å R-free 0.237 |
| 5OXI C-terminally retracted ubiquitin L67S mutant Deposited 2017-09-06 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Mutation：L67S | SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；3 M ammonium sulfate, 0.1 M MES (pH 6.0); 2:1 protein to reservoir ratio
|
Resolution 1.63 Å R-free 0.237 |
| 5WQ4 Crystal structure of OPTN and linear diubiquitin complex Deposited 2016-11-23 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–152（152 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；289.15 K；30% w/v PEG 3350, 0.1 M HEPES (pH 7.5)
|
Resolution 3.00 Å R-free 0.303 |
| 5WQ4 Crystal structure of OPTN and linear diubiquitin complex Deposited 2016-11-23 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–152（152 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；289.15 K；30% w/v PEG 3350, 0.1 M HEPES (pH 7.5)
|
Resolution 3.00 Å R-free 0.303 |
| 5ZQ3 PDE-Ubiquitin Deposited 2018-04-17 | Different construct Different oligomeric state Different experimental method 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；293 K；PEG 10000, Bicine
|
Resolution 2.18 Å R-free 0.213 |
| 5ZQ3 PDE-Ubiquitin Deposited 2018-04-17 | Different construct Different oligomeric state Different experimental method 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；293 K；PEG 10000, Bicine
|
Resolution 2.18 Å R-free 0.213 |
| 5ZQ4 PDE-Ubi-ADPr Deposited 2018-04-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–76（76 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；PEG 10000, Bicine
|
Resolution 2.22 Å R-free 0.226 |
| 5ZQ4 PDE-Ubi-ADPr Deposited 2018-04-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 | AMP ADENOSINE MONOPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；PEG 10000, Bicine
|
Resolution 2.22 Å R-free 0.226 |
| 5ZQ5 SidE-Ubi Deposited 2018-04-17 | Different construct Different mutation/modification Different oligomeric state 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 D
1–76（76 aa）
|
Mutation：R42A Mutation：R42A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350, Tacsimate
|
Resolution 2.49 Å R-free 0.233 |
| 5ZQ6 SidE-Ubi-ADPr Deposited 2018-04-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–76（76 aa）
Chain D
1–76（76 aa）
|
Mutation：R42A Mutation：R42A | ADP ADENOSINE-5'-DIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350, Tacsimate
|
Resolution 3.01 Å R-free 0.232 |
| 5ZQ7 SidE-Ubi-NAD Deposited 2018-04-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–76（76 aa）
Chain D
1–76（76 aa）
|
Mutation：R42A Mutation：R42A | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 AMP ADENOSINE MONOPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350, Tacsimate
|
Resolution 2.85 Å R-free 0.239 |
| 6A43 R1EN(5-225)-ubiquitin fusion Deposited 2018-06-19 | 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 Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Mutation：E44A, A73C | ACY ACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；2.0M sodium acetate, 10mM ammonium sulfate, 1% Jeffamine M600
|
Resolution 2.40 Å R-free 0.241 |
| 6A44 R1EN(5-227)-ubiquitin fusion Deposited 2018-06-19 | 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 Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
77–152（76 aa）
|
Mutation：E44A, A73C | ACY ACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.3；283 K；2.0 M sodium acetate, 10 mM ammonium sulfate, 1% Jeffamine M600
|
Resolution 2.40 Å R-free 0.237 |
| 6AQR SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin Deposited 2017-08-21 | Different construct 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 D
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M HEPES pH 7.0
17% PEG3350
0.1 M ammonium sulfate
|
Resolution 2.10 Å R-free 0.249 |
| 6B7M Crystal structure of Legionella effector sdeD (lpg2509) in complex with Ubiquitin Deposited 2017-10-04 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–76（76 aa）
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 7；298 K；200 mM NaCl, 100 mM Imidazole pH 7.0, 24% PEG 8000
|
Resolution 1.70 Å R-free 0.196 |
| 6B7O Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with ADP-ribosylated Ubiquitin Deposited 2017-10-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–76（76 aa）
Chain C
1–76（76 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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM Na Cacodylate pH 7.0, 21% PEG 8000
|
Resolution 1.85 Å R-free 0.201 |
| 6EQI Structure of PINK1 bound to ubiquitin Deposited 2017-10-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–76（76 aa）
|
Mutation：T66V L67N | GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295.15 K；The PhPINK1-Nb696-Ub TVLN complex was crystallised at 7 mg/ml using sitting-drop vapour diffusion against 1.3 M Ammonium Tartrate Dibasic, 0.1 M BIS-TRIS Propane pH 7.0 from a 1:1 protein to mother liquor ratio, in 100 nl drops at 295.15 K. Crystals were optimised using streak seeding with a cat whisker at 8.9 mg/ml complex concentration in 1.4 M Ammonium Tartrate, 0.1 M BIS-TRIS Propane pH 6.3 at 295.15 K.
|
Resolution 3.10 Å R-free 0.234 |
| 6K2U Crystal structure of Thr66 ADP-ribosylated ubiquitin Deposited 2019-05-15 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 ZN ZINC ION × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.1M MMT (Malic Acid, MES and TRIS (1:2:2 Molar Ratio), pH 5.5 adjusted with HCl), 0.1M magnesium chloride, 0.1M zinc acetate 12% PEG8000
|
Resolution 2.55 Å R-free 0.247 |
| 6KBE Structure of Deubiquitinase Deposited 2019-06-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
1–152（152 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；291 K；0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
|
Resolution 2.34 Å R-free 0.256 |
| 6N13 UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin Deposited 2018-11-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 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 |
| 6N6R Crystal structure of ABIN-1 UBAN in complex with two M1-linked di-ubiquitins Deposited 2018-11-27 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
76–228（153 aa）
Chain C
76–228（153 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30% v/v PEG-MME550, 0.1 M bis-tris pH 6.5, and 0.05 M calcium chloride dihydrate
|
Resolution 1.95 Å R-free 0.278 |
| 6NQA Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex Deposited 2019-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain L
1–76（76 aa）
|
Mutation：G76C | SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions
Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
|
Resolution 3.54 Å |
| 6NXK Ubiquitin binding variants Deposited 2019-02-08 | Different construct Different oligomeric state 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 | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1M HEPES pH 7.7, 27.5% PEG3350, 2.5mM APC2 WHB (735-C) + 2.08mM Ubiquitin protein co-mixed
|
Resolution 2.20 Å R-free 0.266 |
| 6NXK Ubiquitin binding variants Deposited 2019-02-08 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 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；277.15 K；0.1M HEPES pH 7.7, 27.5% PEG3350, 2.5mM APC2 WHB (735-C) + 2.08mM Ubiquitin protein co-mixed
|
Resolution 2.20 Å R-free 0.266 |
| 6OI4 RPN13 (19-132)-RPN2 (940-952) pY950-Ub complex Deposited 2019-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–76（76 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 6 |
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 1.76 Å R-free 0.207 |
| 6OI4 RPN13 (19-132)-RPN2 (940-952) pY950-Ub complex Deposited 2019-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 | EDO 1,2-ETHANEDIOL × 3 |
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 1.76 Å R-free 0.207 |
| 6P5B Crystal Structure of MavC in Complex with Ub-UbE2N Deposited 2019-05-30 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.2 M Na Malonate, 25% PEG 3350, 10 mM NiCl2
|
Resolution 2.10 Å R-free 0.232 |
| 6Q00 TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1 Deposited 2019-08-01 | Different construct Different oligomeric state 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 | K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；10 mM Tris, 200 mM Potassium Formate, 14% (w/v) PEG 3350
|
Resolution 0.85 Å R-free 0.112 |
| 6QML UCHL3 in complex with synthetic, K27-linked diubiquitin Deposited 2019-02-07 | 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 | 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
1–76（76 aa）
|
Not recorded | 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 |
| 6RYA Structure of Dup1 mutant H67A:Ubiquitin complex Deposited 2019-06-10 | Different construct Different oligomeric state Different experimental method 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；pH 8；293 K；20 - 22.5 % PEG 3350/ PEG4000, 100 mM Tris-HCl pH 8.0, 100 mM Magnesium chloride
|
Resolution 2.21 Å R-free 0.289 |
| 6RYA Structure of Dup1 mutant H67A:Ubiquitin complex Deposited 2019-06-10 | Different construct Different oligomeric state Different experimental method 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, SITTING DROP；pH 8；293 K；20 - 22.5 % PEG 3350/ PEG4000, 100 mM Tris-HCl pH 8.0, 100 mM Magnesium chloride
|
Resolution 2.21 Å R-free 0.289 |
| 6RYA Structure of Dup1 mutant H67A:Ubiquitin complex Deposited 2019-06-10 | Different construct Different oligomeric state Different experimental method 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, SITTING DROP；pH 8；293 K；20 - 22.5 % PEG 3350/ PEG4000, 100 mM Tris-HCl pH 8.0, 100 mM Magnesium chloride
|
Resolution 2.21 Å R-free 0.289 |
| 6S53 Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate Deposited 2019-06-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain D
1–76（76 aa）
Chain F
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；Crystals grew in 0.1 M Tris/BICINE pH 8.5, 10.5 % (w/v) PEG3350/PEG 1K/MPD and 0.08 M sodium nitrate/sodium phosphate/ammonium sulfate.
|
Resolution 2.80 Å R-free 0.249 |
| 6S53 Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate Deposited 2019-06-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain J
1–76（76 aa）
Chain L
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；Crystals grew in 0.1 M Tris/BICINE pH 8.5, 10.5 % (w/v) PEG3350/PEG 1K/MPD and 0.08 M sodium nitrate/sodium phosphate/ammonium sulfate.
|
Resolution 2.80 Å R-free 0.249 |
| 6SQR Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub Deposited 2019-09-04 | Different construct 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 I
1–76（76 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 12 ZN ZINC ION × 8 NO3 NITRATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；292 K；0.1 M Tris-HCl, pH 8.5, 20% (v/v) PEG Smear High
|
Resolution 2.18 Å R-free 0.227 |
| 6T7F RCR E3 ligase E2-Ubiquitin transthiolation intermediate Deposited 2019-10-21 | 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
1–73（73 aa）
|
Not recorded | ZN ZINC ION × 6 LWZ 3,3-bis(sulfanyl)-~{N}-(1~{H}-1,2,3-triazol-4-ylmethyl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；0.85 M sodium citrate, 100 mM sodium chloride, 100 mM Tris-HCl pH 8.0
|
Resolution 2.58 Å R-free 0.256 |
| 6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28 | 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: pentadecameric |
Chain O
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 4 seconds before plunging
|
Resolution 3.60 Å |
| 6TNF Structure of monoubiquitinated FANCD2 in complex with FANCI and DNA Deposited 2019-12-07 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric |
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；50 mM HEPES, 100 mM imidazole, 150 mM NaCl, 1 mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6TTU Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 Deposited 2019-12-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain U
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.70 Å |
| 6TUV Crystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin Deposited 2020-01-08 | 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 × 3 PDB declaration: trimeric |
Chain D
1–76（76 aa）
Chain H
1–76（76 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；100 mM Tris-HCl, 200mM LiSO4.H2O, 30% PEG400
|
Resolution 2.16 Å R-free 0.249 |
| 6TUV Crystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin Deposited 2020-01-08 | Different construct Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain L
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；100 mM Tris-HCl, 200mM LiSO4.H2O, 30% PEG400
|
Resolution 2.16 Å R-free 0.249 |
| 6TXB Crystal structure of Mindy1 mutant (P138A) in complex with Lys48 linked di-ubiquitin Deposited 2020-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
1–76（76 aa）
Chain H
1–76（76 aa）
|
Not recorded | NA SODIUM ION × 4 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.2 M Sodium malonate, 20% PEG 3350
|
Resolution 2.18 Å R-free 0.246 |
| 6TXB Crystal structure of Mindy1 mutant (P138A) in complex with Lys48 linked di-ubiquitin Deposited 2020-01-14 | Different construct Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain L
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；293.15 K；0.2 M Sodium malonate, 20% PEG 3350
|
Resolution 2.18 Å R-free 0.246 |
| 6ULH Structure of MavC in complex with its substrate in R3 spacegroup Deposited 2019-10-08 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；0.1 M Sodium Acetate: HCl, pH 4.6
3.5 M Sodium Formate
|
Resolution 1.97 Å R-free 0.227 |
| 6UMP Crystal structure of MavC in complex with substrate mimic in P65 space group Deposited 2019-10-10 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Sodium formate, 20% w/v Polyethylene glycol 3,350
|
Resolution 2.80 Å R-free 0.304 |
| 6UMS Crystal structure of MavC in complex with its substrate mimic in C222(1) space group Deposited 2019-10-10 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
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；0.15 M Potassium bromide, 30% (w/v) PEG 2000 MME
|
Resolution 2.34 Å R-free 0.250 |
| 6V5D EROS3 RDC and NOE Derived Ubiquitin Ensemble Deposited 2019-12-04 | Different construct Different experimental conditions | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；308 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition
0.9 mM [U-100% 13C; U-100% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 6VAE Mono-ubiquitinated Fanconi Anemia ID complex bound to ICL DNA Deposited 2019-12-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric |
Chain C
1–76（76 aa）
Chain D
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 3.60 Å |
| 6VAF Structure of mono-ubiquitinated FANCD2 bound to non-ubiquitinated FANCI and to DNA Deposited 2019-12-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric |
Chain D
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 3.90 Å |
| 6VEN Yeast COMPASS in complex with a ubiquitinated nucleosome Deposited 2020-01-02 | 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 × 16 PDB declaration: octadecameric |
Chain K
1–76（76 aa）
|
Mutation：G76C | ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot force 5
3.5 sec blot time
|
Resolution 3.37 Å |
| 6W9D RNF12 RING domain in complex with a Ube2d2~Ub conjugate Deposited 2020-03-22 | 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 | ZN ZINC ION × 2 IOD IODIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；15-20% PEG 3350,
200-400 mM NaI
|
Resolution 3.19 Å R-free 0.281 |
| 6W9D RNF12 RING domain in complex with a Ube2d2~Ub conjugate Deposited 2020-03-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 2 IOD IODIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；15-20% PEG 3350,
200-400 mM NaI
|
Resolution 3.19 Å R-free 0.281 |
| 6W9D RNF12 RING domain in complex with a Ube2d2~Ub conjugate Deposited 2020-03-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 2 IOD IODIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；15-20% PEG 3350,
200-400 mM NaI
|
Resolution 3.19 Å R-free 0.281 |
| 6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain M
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
|
Resolution 1.82 Å R-free 0.208 |
| 6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain V
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
|
Resolution 1.82 Å R-free 0.208 |
| 6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain W
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
|
Resolution 1.82 Å R-free 0.208 |
| 6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain X
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
|
Resolution 1.82 Å R-free 0.208 |
| 6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain N
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
|
Resolution 1.82 Å R-free 0.208 |
| 6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain O
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
|
Resolution 1.82 Å R-free 0.208 |
| 6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
|
Resolution 1.82 Å R-free 0.208 |
| 6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
|
Resolution 1.82 Å R-free 0.208 |
| 6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain R
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
|
Resolution 1.82 Å R-free 0.208 |
| 6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain S
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
|
Resolution 1.82 Å R-free 0.208 |
| 6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain T
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
|
Resolution 1.82 Å R-free 0.208 |
| 6W9R Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain U
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 6K, 0.1 M citrate pH 4.6
|
Resolution 1.82 Å R-free 0.208 |
| 6W9S Crystal structure of an OTU deubiquitinase from Escherichia albertii bound to ubiquitin Deposited 2020-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FMT FORMIC ACID × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.8 M sodium formate, 10% PEG 8K, 10% PEG 1K, 0.1 M sodium acetate pH 4.5
|
Resolution 2.10 Å R-free 0.253 |
| 6WJD SA-like state of human 26S Proteasome with non-cleavable M1-linked hexaubiquitin and E3 ubiquitin ligase E6AP/UBE3A Deposited 2020-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric |
Chain u
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM Tris, pH 7.5, 50 mM NaCl, 1.5 mM ATP-gamma-S, 5 mM MgCl2, 2 mM DTT, 10 uM zinc sulfate
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 6WKR PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome Deposited 2020-04-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: octadecameric |
Chain F
1–76（76 aa）
Chain T
1–76（76 aa）
|
Not recorded | MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 6WTG SdeA DUB Domain in complex with Ubiquitin Deposited 2020-05-02 | Different construct Different oligomeric state Different experimental method 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 9；298 K；0.1 M bicine pH 9.0, 65% (v/v) MPD
|
Resolution 2.63 Å R-free 0.243 |
| 6YPT X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with Ubiquitin Deposited 2020-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
77–151（75 aa）
|
Not recorded | GVE METHYL 4-AMINOBUTANOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；21% PEG-20K + 0.1M MES-NaOH pH6.5
|
Resolution 3.66 Å R-free 0.283 |
| 6YPT X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with Ubiquitin Deposited 2020-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
77–151（75 aa）
|
Not recorded | GVE METHYL 4-AMINOBUTANOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；21% PEG-20K + 0.1M MES-NaOH pH6.5
|
Resolution 3.66 Å R-free 0.283 |
| 6Z7V Crystal structure of Mindy2 (C266A) in complex with Lys48 linked di-ubiquitin (K48-Ub2) Deposited 2020-06-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
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）
|
Not recorded | K POTASSIUM ION × 4 PG4 TETRAETHYLENE GLYCOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；50 mM potassium phosphate monobasic, 14% PEG 8000
|
Resolution 2.65 Å R-free 0.254 |
| 7B5L Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 Deposited 2020-12-04 | Different construct 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 U
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7B5M Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2 Deposited 2020-12-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain U
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.91 Å |
| 7B5N Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. Deposited 2020-12-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain U
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7BBD Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2 Deposited 2020-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
1–76（76 aa）
|
Mutation：G75A, G76A | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；290.15 K；MOPSO, Bis-Tris, PEG 4K, 1,2,6-hexanetriol, Li, Na, K
|
Resolution 2.20 Å R-free 0.252 |
| 7BBF Crystal structure of ubiquitin charged Ube2N (Ube2N~Ub) in complex with Ube2V2 Deposited 2020-12-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain C
1–76（76 aa）
Chain F
1–76（76 aa）
Chain I
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；290 K；0.1 M bicine Trizma base pH 8.5, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.2 % of each Anesthetic alkaloids (lidocaine HCl H2O, procaine HCl, proparacaine HCl, tetracaine HCl)
|
Resolution 2.54 Å R-free 0.253 |
| 7BXG MavC-UBE2N-Ub complex Deposited 2020-04-19 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.1 M sodium malonate, pH 7.0, 12% PEG3350
|
Resolution 2.71 Å R-free 0.243 |
| 7EAL The structure of the A20-Binding Inhibitor of NF-kB 1 in complex with di-ubiquitin Deposited 2021-03-07 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–152（152 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；255 K；0.1M Citrate pH 5.5, 10% Iso-propanol, 20% PEG 400
|
Resolution 2.50 Å R-free 0.224 |
| 7EAL The structure of the A20-Binding Inhibitor of NF-kB 1 in complex with di-ubiquitin Deposited 2021-03-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
1–152（152 aa）
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；255 K；0.1M Citrate pH 5.5, 10% Iso-propanol, 20% PEG 400
|
Resolution 2.50 Å R-free 0.224 |
| 7EAO The structure of the A20-binding inhibitor of NF-kB 1 in complex with tri-ubiquitin Deposited 2021-03-07 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–228（228 aa）
Fragment：UNP residues 1-228
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Potassium citrate tribasic, 20% PEG 3350
|
Resolution 2.90 Å R-free 0.283 |
| 7EB9 The structure of the A20-binding inhibitor of NF-kB 1 in complex with tetra-ubiquitin Deposited 2021-03-09 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–304（304 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1 M Sodium malonate pH 6.0, 10% PEG 3350
|
Resolution 3.20 Å R-free 0.264 |
| 7JXV ANTH domain of CALM (clathrin-assembly lymphoid myeloid leukemia protein) bound to ubiquitin Deposited 2020-08-28 | Different construct Different oligomeric state Different experimental method 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 6；277 K；0.1 M MES, pH 6, 0.2 M NaCl, 20% w/v MPEG2000
|
Resolution 2.35 Å R-free 0.264 |
| 7K6P Active state Dot1 bound to the unacetylated H4 nucleosome Deposited 2020-09-21 | 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 × 10 PDB declaration: dodecameric |
Chain L
1–76（76 aa）
|
Mutation：G76C | SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7K6Q Active state Dot1 bound to the H4K16ac nucleosome Deposited 2020-09-21 | 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 × 10 PDB declaration: dodecameric |
Chain L
1–76（76 aa）
|
Mutation：G76C | SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7KEO Crystal structure of K29-linked di-ubiquitin in complex with synthetic antigen binding fragment Deposited 2020-10-11 | 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
1–76（76 aa）
Chain D
1–76（76 aa）
|
Not recorded | PO4 PHOSPHATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M phosphate-citriate, 40% v/v Polyethylene glycol 300
|
Resolution 2.90 Å R-free 0.282 |
| 7KEO Crystal structure of K29-linked di-ubiquitin in complex with synthetic antigen binding fragment Deposited 2020-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
1–76（76 aa）
Chain H
1–76（76 aa）
|
Not recorded | PO4 PHOSPHATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M phosphate-citriate, 40% v/v Polyethylene glycol 300
|
Resolution 2.90 Å R-free 0.282 |
| 7M4M Crystal structure of RBR E3 ligase RNF216 with ubiquitin Deposited 2021-03-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 × 5 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；15% PEG 6000, 0.18 M NaCl, 0.09 M Na HEPES pH7.0, 0.1 M KCl
|
Resolution 2.39 Å R-free 0.247 |
| 7M4M Crystal structure of RBR E3 ligase RNF216 with ubiquitin Deposited 2021-03-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 | ZN ZINC ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；15% PEG 6000, 0.18 M NaCl, 0.09 M Na HEPES pH7.0, 0.1 M KCl
|
Resolution 2.39 Å R-free 0.247 |
| 7M4N Crystal structure of RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin Deposited 2021-03-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–76（76 aa）
Chain E
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 3 SO4 SULFATE ION × 4 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.9；293 K；0.2M ammonium sulfate, 30% PEG 4000
|
Resolution 2.52 Å R-free 0.273 |
| 7M4N Crystal structure of RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin Deposited 2021-03-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
1–76（76 aa）
Chain F
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 3 SO4 SULFATE ION × 4 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.9；293 K；0.2M ammonium sulfate, 30% PEG 4000
|
Resolution 2.52 Å R-free 0.273 |
| 7M4O Crystal structure of phosphorylated RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin Deposited 2021-03-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 3 SO4 SULFATE ION × 3 GOL GLYCEROL × 3 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.22；293 K；0.259 M ammonium sulfate, 30.1 % PEG monomethyl ether 2000, 0.1M sodium acetate-acetic acid pH 5.22
|
Resolution 2.21 Å R-free 0.252 |
| 7MEX Structure of yeast Ubr1 in complex with Ubc2 and 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 × 4 PDB declaration: tetrameric |
Chain C
1–76（76 aa）
|
Mutation：G76C | ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 7MIC Maize rayado fino virus protease in complex with Ubiquitin Deposited 2021-04-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 2 3CN 3-AMINOPROPANE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 3.8；277 K；100 mM phosphate citrate buffer (pH 3.8), 200 mM lithium sulfate and 25 % PEG 1000
|
Resolution 2.09 Å R-free 0.263 |
| 7MYF Ubiquitin variant UbV.k.1 in complex with Ube2k Deposited 2021-05-21 | Different construct Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
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；289 K；0.2-0.3 M ammonium citrate dibasic, 20-25% PEG3350
|
Resolution 3.00 Å R-free 0.293 |
| 7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
Chain E
1–76（76 aa）
Chain F
1–76（76 aa）
|
Not recorded | CL CHLORIDE ION × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt
0.1 M BICINE pH 8.5
15% w/v PEG 20,000
|
Resolution 2.81 Å R-free 0.288 |
| 7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
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 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt
0.1 M BICINE pH 8.5
15% w/v PEG 20,000
|
Resolution 2.81 Å R-free 0.288 |
| 7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain N
1–76（76 aa）
Chain O
1–76（76 aa）
Chain P
1–76（76 aa）
Chain Q
1–76（76 aa）
Chain R
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt
0.1 M BICINE pH 8.5
15% w/v PEG 20,000
|
Resolution 2.81 Å R-free 0.288 |
| 7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain T
1–76（76 aa）
Chain U
1–76（76 aa）
Chain V
1–76（76 aa）
Chain W
1–76（76 aa）
Chain X
1–76（76 aa）
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt
0.1 M BICINE pH 8.5
15% w/v PEG 20,000
|
Resolution 2.81 Å R-free 0.288 |
| 7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain Z
1–76（76 aa）
Chain a
1–76（76 aa）
Chain b
1–76（76 aa）
Chain c
1–76（76 aa）
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；293.15 K；3% w/v Dextran sulphate sodium salt
0.1 M BICINE pH 8.5
15% w/v PEG 20,000
|
Resolution 2.81 Å R-free 0.288 |
| 7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
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）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt
0.1 M BICINE pH 8.5
15% w/v PEG 20,000
|
Resolution 2.81 Å R-free 0.288 |
| 7NPI Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) Deposited 2021-02-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain l
1–76（76 aa）
Chain m
1–76（76 aa）
Chain n
1–76（76 aa）
Chain o
1–76（76 aa）
Chain p
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；3% w/v Dextran sulphate sodium salt
0.1 M BICINE pH 8.5
15% w/v PEG 20,000
|
Resolution 2.81 Å R-free 0.288 |
| 7OWD Structure of CYLD CAP-Gly3 (467-552) bound to Ub; tetragonal space group Deposited 2021-06-17 | Different construct Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 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, SITTING DROP；pH 4.2；291 K；40 (v/v) PEG 300, 100 mM phosphate/citrate pH 4.2
|
Resolution 1.71 Å R-free 0.245 |
| 7R70 Crystal Structure of the UbArk2C fusion protein Deposited 2021-06-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289.15 K；1.6 M tri-sodium citrate
|
Resolution 2.50 Å R-free 0.245 |
| 7R70 Crystal Structure of the UbArk2C fusion protein Deposited 2021-06-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289.15 K；1.6 M tri-sodium citrate
|
Resolution 2.50 Å R-free 0.245 |
| 7R71 Crystal Structure of the UbArk2C-UbcH5b~Ub complex Deposited 2021-06-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–76（76 aa）
Chain D
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1 M MMT pH 6.0, 25% w/v PEG 1500
|
Resolution 2.80 Å R-free 0.271 |
| 7TV4 Crystal structure of NEMO CoZi in complex with HOIP NZF1 and linear diubiquitin Deposited 2022-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
77–228（152 aa）
Chain G
77–228（152 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, pH 8.5, 22% v/v PEG Smear Broad
|
Resolution 4.20 Å R-free 0.286 |
| 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 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 B
1–76（76 aa）
|
Not recorded | 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 |
| 7UYH Structure of the first OTU domain from Legionella pneumophila effector protein LotA bound to K6-linked diUb Deposited 2022-05-06 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–76（76 aa）
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 5.5；293 K；25% PEG 3350, 10% ethylene glycol, 0.2 M KSCN, 0.1 M MES pH 5.5
|
Resolution 2.80 Å R-free 0.262 |
| 7YUI Crystal structure of HOIL-1L(195-423) in complex with the linear tetra-ubiquitin Deposited 2022-08-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
77–380（304 aa）
|
Not recorded | ZN ZINC ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Lithium chloride, 0.1 M Tris(pH 8), 20 %(w/v)PEG 8000
|
Resolution 2.60 Å R-free 0.258 |
| 7ZJ3 Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate Deposited 2022-04-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain F
76–152（77 aa）
Chain L
76–152（77 aa）
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5
10% (w/v) PEG 8K
|
Resolution 2.53 Å R-free 0.258 |
| 7ZJ3 Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate Deposited 2022-04-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain C
76–152（77 aa）
Chain I
76–152（77 aa）
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5
10% (w/v) PEG 8K
|
Resolution 2.53 Å R-free 0.258 |
| 8A9J Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 without ML323 (consensus reconstruction) Deposited 2022-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric |
Chain C
77–152（76 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；blotted for 3.0 secs before plunging
|
Resolution 2.80 Å |
| 8A9K Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with ML323 (consensus reconstruction) Deposited 2022-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric |
Chain C
77–152（76 aa）
|
Not recorded | ZN ZINC ION × 1 JDA 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 8AMS Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin Deposited 2022-08-04 | 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 E
76–152（77 aa）
|
Not recorded | GOL GLYCEROL × 9 ZN ZINC ION × 4 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.2 M sodium formate, 0.1 M bis-tris propane, 20% PEG 3350
|
Resolution 2.40 Å R-free 0.233 |
| 8B3G C(N)RL4CSA-UVSSA-E2-ubiquitin complex. Deposited 2022-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain U
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 8B3I CRL4CSA-E2-Ub (state 2) Deposited 2022-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain U
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8E7O CRYSTAL STRUCTURE OF LYS48-LINKED TETRAUBIQUITIN Deposited 2022-08-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
|
Mutation：K48R | SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295.15 K；25% w/v PEG 3350, 0.2M ammonium sulfate, 0.1M Bis-Tris pH 5.5
|
Resolution 1.70 Å R-free 0.221 |
| 8EAZ HOIL-1/E2-Ub/Ub transthiolation complex Deposited 2022-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
1–76（76 aa）
Chain G
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；28% PEG smear broad, 0.2 M sodium chloride, 0.1 M sodium phosphate, pH 6.2
|
Resolution 3.08 Å R-free 0.266 |
| 8EAZ HOIL-1/E2-Ub/Ub transthiolation complex Deposited 2022-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
1–76（76 aa）
Chain H
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；28% PEG smear broad, 0.2 M sodium chloride, 0.1 M sodium phosphate, pH 6.2
|
Resolution 3.08 Å R-free 0.266 |
| 8EB0 RNF216/E2-Ub/Ub transthiolation complex Deposited 2022-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 7 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.9；293 K；2 M ammonium sulfate
|
Resolution 3.03 Å R-free 0.339 |
| 8FTQ Crystal structure of hRpn13 Pru domain in complex with Ubiquitin and XL44 Deposited 2023-01-13 | 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
1–72（72 aa）
Chain D
1–72（72 aa）
|
Not recorded | ZTO N-(3-{[(3R)-5-fluoro-2-oxo-2,3-dihydro-1H-indol-3-yl]methyl}phenyl)-4-methoxybenzamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 4.6；277 K；0.1 M Citric acid pH 4.6 and 20% PEG4000
|
Resolution 2.10 Å R-free 0.247 |
| 8K6I LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 | 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 × 6 PDB declaration: hexameric |
Chain E
1–76（76 aa）
Chain F
1–76（76 aa）
|
Not recorded | PO4 PHOSPHATE ION × 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, PEG8000, HEPES
|
Resolution 3.19 Å R-free 0.315 |
| 8OFF Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1) Deposited 2023-03-15 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric |
Chain Fa
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；blot force = 0 N
blot time = 8 s
|
Resolution 3.40 Å |
| 8PJN Catalytic module of human CTLH E3 ligase bound to multiphosphorylated UBE2H~ubiquitin Deposited 2023-06-23 | 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 u
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8PMQ Catalytic module of yeast GID E3 ligase bound to multiphosphorylated Ubc8~ubiquitin Deposited 2023-06-29 | 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 U
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.53 Å |
| 8PQL K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide Deposited 2023-07-11 | 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 × 8 PDB declaration: nonameric |
Chain E
1–685（685 aa）
Chain U
1–685（685 aa）
|
Mutation：K48C,S455P L456T L457Q K458G E459R L460A Mutation：K48C | SY8 5-azanylpentan-2-one × 1 ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.76 Å |
| 8Q7R Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide Deposited 2023-08-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain U
1–685（685 aa）
|
Not recorded | U9O 5-azanyl-1-oxidanyl-pentan-2-one × 1 ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.71 Å |
| 8R5H Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2 Deposited 2023-11-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain U
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 3 SY8 5-azanylpentan-2-one × 1 759 (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 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.44 Å |
| 8SSI Structure of Burkholderia pseudomallei deubiquitinase TssM in complex with ubiquitin Deposited 2023-05-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–75（75 aa）
|
Not recorded | GOL GLYCEROL × 1 AYE prop-2-en-1-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 5.6
|
Resolution 2.50 Å R-free 0.254 |
| 8SSI Structure of Burkholderia pseudomallei deubiquitinase TssM in complex with ubiquitin Deposited 2023-05-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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；295 K；1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 5.6
|
Resolution 2.50 Å R-free 0.254 |
| 8ST7 Structure of E3 ligase VsHECT bound to ubiquitin Deposited 2023-05-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 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, HANGING DROP；295 K；20% PEG 2K MME, 0.1 M MES pH 6.0, and 20% ethylene glycol
|
Resolution 1.44 Å R-free 0.199 |
| 8ST7 Structure of E3 ligase VsHECT bound to ubiquitin Deposited 2023-05-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 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；295 K；20% PEG 2K MME, 0.1 M MES pH 6.0, and 20% ethylene glycol
|
Resolution 1.44 Å R-free 0.199 |
| 8ST8 Structure of E3 ligase SopA bound to ubiquitin Deposited 2023-05-09 | Different construct Different oligomeric state 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）
|
Not recorded | AYE prop-2-en-1-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；22.5% PEG 8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 7.0, and 20% glycerol
|
Resolution 1.75 Å R-free 0.196 |
| 8ST9 Structure of E3 ligase NleL bound to ubiquitin Deposited 2023-05-09 | Different construct Different oligomeric state 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）
|
Not recorded | AYE prop-2-en-1-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；20% PEG 3350, 0.2 M KSCN, 0.1 M bis-tris propane pH 7.5, 20% glycerol, and 10% ethylene glycol
|
Resolution 2.50 Å R-free 0.252 |
| 8ST9 Structure of E3 ligase NleL bound to ubiquitin Deposited 2023-05-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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；295 K；20% PEG 3350, 0.2 M KSCN, 0.1 M bis-tris propane pH 7.5, 20% glycerol, and 10% ethylene glycol
|
Resolution 2.50 Å R-free 0.252 |
| 8SVF BAP1/ASXL1 bound to the H2AK119Ub Nucleosome Deposited 2023-05-16 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric |
Chain M
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 3.20 Å |
| 8T48 The N4BP1 CUE-like domain in complex with linear di-Ubiquitin Deposited 2023-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–152（152 aa）
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tris pH 8.5, 30% (w/v) PEG 4K, 0.2 M Li2SO4
|
Resolution 2.00 Å R-free 0.218 |
| 8T48 The N4BP1 CUE-like domain in complex with linear di-Ubiquitin Deposited 2023-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–152（152 aa）
|
Not recorded | LI LITHIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tris pH 8.5, 30% (w/v) PEG 4K, 0.2 M Li2SO4
|
Resolution 2.00 Å R-free 0.218 |
| 8U5H Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome Deposited 2023-09-12 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain D
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 3.23 Å |
| 9D1Y Structure of G75R Ubiquitin bound to KLHDC3-EloB/C Deposited 2024-08-08 | 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 × 4 PDB declaration: tetrameric |
Chain D
1–76（76 aa）
|
Mutation：G75R | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；10%PEG5KMME,
5% Tacsimate pH=7.0,
0.1M HEPES pH=7.0
|
Resolution 2.60 Å R-free 0.216 |
| 9D1Z Structure of G75Q Ubiquitin bound to KLHDC3-EloB/C Deposited 2024-08-08 | 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 × 4 PDB declaration: tetrameric |
Chain D
1–76（76 aa）
|
Mutation：G75Q | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；10%%KMME,
5% Tacsimate pH=7.0,
0.1M HEPES 7.0
|
Resolution 1.88 Å R-free 0.190 |
| 9D8P Focused map of Cryo-EM structure of Ubiquitin C-degron bound to KLHDC10-EloB/C Deposited 2024-08-19 | Different construct Different mutation/modification Different oligomeric state 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：K48C | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9DI1 Cryo-EM structure of the USP1-UAF1-Ubiquitin complex inhibited by KSQ-4279 Deposited 2024-09-04 | 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
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 A1IB8 6-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-1-[[4-[1-propan-2-yl-4-(trifluoromethyl)imidazol-2-yl]phenyl]methyl]pyrazolo[3,4-d]pyrimidine × 1 A1A4Y 3-(methanesulfonyl)propan-1-amine × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 9DI2 Cryo-EM structure of the USP1-UAF1-Ubiquitin-VS complex Deposited 2024-09-04 | 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
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 A1A4Y 3-(methanesulfonyl)propan-1-amine × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 9DNS Cryo-EM structure of Tom1-UBE2D2-ubiquitin complex Deposited 2024-09-18 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain U
1–76（76 aa）
Chain V
1–76（76 aa）
Chain W
1–76（76 aa）
Chain X
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2；30 mM HEPES pH 7.2, 200 mM NaCl, 0.5 mM TCEP, 0.2 mM CHAPSO
cryo-EM vitrification conditions
Cryogen ETHANE；CHAPSO detergent added to final conc. of 0.2 mM. Sample applied twice.
|
Resolution 2.80 Å |
| 9EGV HOIL-1 RING2 domain bound to ubiquitin Deposited 2024-11-21 | 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
76–152（77 aa）
|
Not recorded | ZN ZINC ION × 6 CL CHLORIDE ION × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；0.01 M magnesium chloride hexahydrate, 0.05 M MES monohydrate pH 6.2, 1.8 M lithium sulfate monohydrate
|
Resolution 2.00 Å R-free 0.208 |
| 9EGV HOIL-1 RING2 domain bound to ubiquitin Deposited 2024-11-21 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: dimeric |
Chain C
76–152（77 aa）
|
Not recorded | ZN ZINC ION × 6 CL CHLORIDE ION × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；0.01 M magnesium chloride hexahydrate, 0.05 M MES monohydrate pH 6.2, 1.8 M lithium sulfate monohydrate
|
Resolution 2.00 Å R-free 0.208 |
| 9EGW HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled) Deposited 2024-11-21 | 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
76–152（77 aa）
|
Not recorded | ZN ZINC ION × 6 CL CHLORIDE ION × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.02 M MgCl2, 0.05 M MES pH6 and 1.8 M LiSO4
|
Resolution 1.78 Å R-free 0.182 |
| 9EGW HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled) Deposited 2024-11-21 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
76–152（77 aa）
|
Not recorded | ZN ZINC ION × 3 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.02 M MgCl2, 0.05 M MES pH6 and 1.8 M LiSO4
|
Resolution 1.78 Å R-free 0.182 |
| 9ERZ Structure of CBL-TKBD bound to Ubiquitin-fused CBLock peptide Deposited 2024-03-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
77–150（74 aa）
Chain D
77–150（74 aa）
|
Not recorded | CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Bis-Tris Propane, pH 6.0, 0.2 M sodium fluoride, and 20% (v/v) PEG 3350
|
Resolution 2.02 Å R-free 0.229 |
| 9FCI USP1 bound to KSQ-4279 and ubiquitin conjugated to FANCD2 (focused refinement) Deposited 2024-05-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
77–152（76 aa）
|
Not recorded | ZN ZINC ION × 1 A1IB8 6-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-1-[[4-[1-propan-2-yl-4-(trifluoromethyl)imidazol-2-yl]phenyl]methyl]pyrazolo[3,4-d]pyrimidine × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9FCJ USP1 bound to ML323 and ubiquitin conjugated to FANCD2 (ordered subset, focused refinement) Deposited 2024-05-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
77–152（76 aa）
|
Not recorded | ZN ZINC ION × 1 JDA 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；blotting for 3.0 seconds
|
Resolution 2.70 Å |
| 9FJ3 Structure of ubiquitin bound of coiled-coil UIM form 2 Deposited 2024-05-30 | 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 A
77–152（76 aa）
|
Not recorded | A1IDH 3-[1-(2-oxidanylideneethyl)-1,2,3-triazol-4-yl]propanal × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；0.1 M amino acids, 0.1 M buffer system 1, pH 6.6-6.7 and 36-38 %(v/v) precipitant mix 1 (Molecular Dimension)
|
Resolution 1.40 Å R-free 0.238 |
| 9FJ3 Structure of ubiquitin bound of coiled-coil UIM form 2 Deposited 2024-05-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 | A1IDH 3-[1-(2-oxidanylideneethyl)-1,2,3-triazol-4-yl]propanal × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；0.1 M amino acids, 0.1 M buffer system 1, pH 6.6-6.7 and 36-38 %(v/v) precipitant mix 1 (Molecular Dimension)
|
Resolution 1.40 Å R-free 0.238 |
| 9FJ4 Structure of ubiquitin bound to coiled coil-UIM form 1 Deposited 2024-05-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
77–152（76 aa）
|
Mutation：contain GSGGS at the N-terminus | A1IDH 3-[1-(2-oxidanylideneethyl)-1,2,3-triazol-4-yl]propanal × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；0.1 M amino acids, 0.1 M buffer system 1, pH 6.6-6.7 and 36-38 %(v/v) precipitant mix 1 (Molecular Dimension)
|
Resolution 1.54 Å R-free 0.266 |
| 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 B
1–75（75 aa）
Chain C
1–76（76 aa）
|
Mutation：K29C | 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 |
| 9GKN Structure of HECT E3 TRIP12 forming K29-linked 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 × 3 PDB declaration: trimeric |
Chain B
1–75（75 aa）
Chain C
77–152（76 aa）
|
Mutation：K29C | SY8 5-azanylpentan-2-one × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.40 Å |
| 9KHS Cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (monomeric conformation) Deposited 2024-11-11 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain D
1–76（76 aa）
Chain E
1–76（76 aa）
|
Mutation：K48C Mutation：K29R | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.31 Å |
| 9KHT cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (dimeric conformation) Deposited 2024-11-11 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric |
Chain D
1–76（76 aa）
Chain d
1–76（76 aa）
|
Mutation：K48C Mutation：K48C | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.85 Å |
| 9M7O Cryo-EM structure of Ufd2/Ubc4-ub complex with K29triUb(monomeric conformation) Deposited 2025-03-10 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain D
1–76（76 aa）
Chain E
1–76（76 aa）
|
Mutation：K48C Mutation：K29R | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.14 Å |
| 9MC4 Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation 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 3.32 Å |
| 9MC5 Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 3 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 3.29 Å |
| 9N1F Crystal Structure of the Ark2C-Ubc13~Ub-Mms2 complex Deposited 2025-01-26 | 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 × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M Sodium Malonate and 18% w/v PEG 3350
|
Resolution 2.10 Å R-free 0.279 |
| 9O4M Crystal structure of Ubiquitin Carboxy Terminal Hydrolase L1 Q209C mutant covalently crosslinked to ubiquitin genetically encoded with N6-(6-bromohexanoyl)-L-lysine Deposited 2025-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–76（76 aa）
|
Not recorded | 6NA HEXANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.1 M DL-Malic acid
|
Resolution 2.00 Å R-free 0.262 |
| 9O4M Crystal structure of Ubiquitin Carboxy Terminal Hydrolase L1 Q209C mutant covalently crosslinked to ubiquitin genetically encoded with N6-(6-bromohexanoyl)-L-lysine Deposited 2025-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 | 6NA HEXANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.1 M DL-Malic acid
|
Resolution 2.00 Å R-free 0.262 |
| 9OVX CRYSTAL STRUCTURE OF UBIQUITIN K27M MUTANT Deposited 2025-06-01 | Different construct Different mutation/modification 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：K27M | CD CADMIUM ION × 6 CL CHLORIDE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；CdCl2 (0.2 M), PEG400 (10% v/v), 2-methyl-2,4-pentanediol (12% v/v) and sodium acetate buffer (0.1 M, pH 4.6)
|
Resolution 1.50 Å R-free 0.154 |
| 9QGG Consensus structure of dUBA1-UbDha-dBIRC6 trapped ternary complex Deposited 2025-03-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
1–76（76 aa）
Chain E
1–76（76 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.58 Å |
| 9QGI Structure of dUBA1-UbDha-dBIRC6 trapped ternary complex (Cluster 2) Deposited 2025-03-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
1–76（76 aa）
Chain E
1–76（76 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 9QGR Structure of dUBA1-UbDha-dBIRC6 trapped ternary complex (Cluster 4) Deposited 2025-03-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
1–76（76 aa）
Chain E
1–76（76 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9QGW Consensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (singly loaded) Deposited 2025-03-14 | 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 | IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 9QH5 Consensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (doubly loaded) Deposited 2025-03-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein 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 3.09 Å |
| 9QIA Structure of UBA6-UbDha-BIRC6 trapped ternary complex (cluster 2) Deposited 2025-03-18 | 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 × 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 4.38 Å |
| 9R85 Cryo-EM structure of the E3 ligase HECTD3 conjugated to ubiquitin Deposited 2025-05-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method 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 | AYE prop-2-en-1-amine × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 9SDX Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub Deposited 2025-08-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain U
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 7 SY8 5-azanylpentan-2-one × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.97 Å |
| 9T7V Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub Deposited 2025-11-12 | 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
1–75（75 aa）
|
Not recorded | FE FE (III) ION × 1 SY8 5-azanylpentan-2-one × 1 ZN ZINC ION × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 9YEA Structure of the isopeptide bond-linked UbcH5b~Ubiquitin conjugate complex for an M1K/C85K UbcH5b mutant Deposited 2025-09-23 | Different construct Different oligomeric state Different experimental method 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；pH 5.5；298 K；0.1 M Sodium Citrate, 20 % (w/v) PEG 3000
|
Resolution 1.83 Å R-free 0.239 |
219 other PDB entries and 348 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | UBC_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–77； UniProt 76–152 |
