Current Protein Identity：P62837
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2CLW Crystal structure of human ubiquitin-conjugating enzyme UbcH5B Deposited 2006-05-02 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–147（147 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 GOL GLYCEROL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 4.6；150 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000
|
Resolution 1.95 Å R-free 0.255 |
| 2CLW Crystal structure of human ubiquitin-conjugating enzyme UbcH5B Deposited 2006-05-02 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–147（147 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 4.6；150 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000
|
Resolution 1.95 Å R-free 0.255 |
| 2CLW Crystal structure of human ubiquitin-conjugating enzyme UbcH5B Deposited 2006-05-02 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–147（147 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 4.6；150 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000
|
Resolution 1.95 Å R-free 0.255 |
| 2CLW Crystal structure of human ubiquitin-conjugating enzyme UbcH5B Deposited 2006-05-02 | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain D
1–147（147 aa）
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 4.6；150 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000
|
Resolution 1.95 Å R-free 0.255 |
| 2ESK Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type Deposited 2005-10-26 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；NaCl, PEG 6000, Sodium Acetate, temperature 294K, pH 4.5, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.36 Å R-free 0.224 |
| 2ESO Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala Deposited 2005-10-26 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：I37A | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；NaCl, PEG 6000, Sodium Acetate, temperature 294K, pH 4.5, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.50 Å R-free 0.219 |
| 2ESP Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala Deposited 2005-10-26 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：I88A | CL CHLORIDE ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；NaCl, PEG 6000, Sodium Acetate, temperature 294K, pH 4.5, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.52 Å R-free 0.233 |
| 2ESQ Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly Deposited 2005-10-26 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：S94G | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；NaCl, PEG 6000, Sodium Acetate, temperature 294K, pH 4.5, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.44 Å R-free 0.205 |
| 3A33 UbcH5b~Ubiquitin Conjugate Deposited 2009-06-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：C85S | GOL GLYCEROL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；2.0M NaCl, 0.1M Potassium acetate, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.280 |
| 3JVZ E2~Ubiquitin-HECT Deposited 2009-09-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
2–147（146 aa）
|
Mutation：L3S, C85S, T98K | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, pH 5.1-5.2, 2.4-2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.30 Å R-free 0.267 |
| 3JVZ E2~Ubiquitin-HECT Deposited 2009-09-17 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
2–147（146 aa）
|
Mutation：L3S, C85S, T98K | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, pH 5.1-5.2, 2.4-2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.30 Å R-free 0.267 |
| 3JW0 E2~Ubiquitin-HECT Deposited 2009-09-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
2–147（146 aa）
|
Mutation：L3S, C85S, T98K | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.10 Å R-free 0.287 |
| 3JW0 E2~Ubiquitin-HECT Deposited 2009-09-17 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
2–147（146 aa）
|
Mutation：L3S, C85S, T98K | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.10 Å R-free 0.287 |
| 3L1Y Crystal structure of human UBC4 E2 conjugating enzyme Deposited 2009-12-14 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–147（147 aa）
Fragment：residues 1-147
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；2M sodium formate, 0.1M sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.60 Å R-free 0.229 |
| 3TGD Crystal structure of the human ubiquitin-conjugating enzyme (E2) UbcH5b Deposited 2011-08-17 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–147（147 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；0.8M potassium phosphate, 0.8M sodium phosphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.203 |
| 3ZNI Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex Deposited 2013-02-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
2–147（146 aa）
Fragment：RESIDUES 2-147
|
Mutation：YES | 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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain G
2–147（146 aa）
Fragment：RESIDUES 2-147
|
Mutation：YES | 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 | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain K
2–147（146 aa）
Fragment：RESIDUES 2-147
|
Mutation：YES | 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 | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain O
2–147（146 aa）
Fragment：RESIDUES 2-147
|
Mutation：YES | 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 |
| 4A49 Structure of phosphoTyr371-c-Cbl-UbcH5B complex Deposited 2011-10-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 K POTASSIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
291 K；20% (W/V) PEG 3350 AND 0.2 M POTASSIUM THIOCYANATE AT 18 DEGREES CELSIUS.
|
Resolution 2.21 Å R-free 0.205 |
| 4A4B Structure of modified phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex Deposited 2011-10-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.5；31-35% PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), 0.2 M KCL, 50 MM HEPES, PH 7.5
|
Resolution 2.79 Å R-free 0.267 |
| 4A4C Structure of phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex Deposited 2011-10-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 CA CALCIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
277 K；50 MM HEPES, PH 7.5, 0.2 M KCL AND 31-35% (V/V) PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH) AT 4 DEGREES CELSIUS.
|
Resolution 2.70 Å R-free 0.268 |
| 4AUQ Structure of BIRC7-UbcH5b-Ub complex. Deposited 2012-05-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain A
1–147（147 aa）
Fragment：UBCH5B, RESIDUES 1-147
Chain D
1–147（147 aa）
Fragment：UBCH5B, RESIDUES 1-147
|
Mutation：YES Mutation：YES | ZN ZINC ION × 4 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 2.18 Å R-free 0.249 |
| 4DDG Crystal structure of human OTUB1/UbcH5b~Ub/Ub Deposited 2012-01-18 | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count |
Chain A
1–147（147 aa）
Chain B
1–147（147 aa）
Chain C
1–147（147 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 | Assembly 2 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count |
Chain J
1–147（147 aa）
Chain K
1–147（147 aa）
Chain L
1–147（147 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 | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count |
Chain A
1–147（147 aa）
Chain B
1–147（147 aa）
Chain C
1–147（147 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 |
| 4LDT The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub Deposited 2013-06-25 | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
1–147（147 aa）
|
Mutation：C85S | 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 |
| 4V3K RNF38-UbcH5B-UB complex Deposited 2014-10-20 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
2–147（146 aa）
Fragment：RESIDUES 2-147
|
Mutation：YES | 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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
2–147（146 aa）
Fragment：RESIDUES 2-147
|
Mutation：YES | 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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
2–147（146 aa）
Fragment：RESIDUES 2-147
|
Mutation：YES | 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 |
| 4WZ3 Crystal structure of the complex between LubX/LegU2/Lpp2887 U-box 1 and Homo sapiens UBE2D2 Deposited 2014-11-18 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：C85S | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；15 mg/ml of E2D2.(C85S)-Ub conjugate and an equimolar concentration of LubX (1-186), 0.2 M sodium tartrate, 0.1 M Tris-Cl (pH 8.5) and 25% PEG3350
|
Resolution 2.70 Å R-free 0.223 |
| 5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：C21S, C85K, C107S, C111S | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
|
Resolution 2.65 Å R-free 0.238 |
| 5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
1–147（147 aa）
|
Mutation：C21S, C85K, C107S, C111S | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
|
Resolution 2.65 Å R-free 0.238 |
| 5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain G
1–147（147 aa）
|
Mutation：C21S, C85K, C107S, C111S | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
|
Resolution 2.65 Å R-free 0.238 |
| 5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–147（147 aa）
|
Mutation：C21S, C85K, C107S, C111S | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
|
Resolution 2.65 Å R-free 0.238 |
| 5D0M Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：C21S, S22R, C85K, C107S, C111S | PO4 PHOSPHATE ION × 1 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；SPG buffer, PEG 1500
|
Resolution 1.91 Å R-free 0.213 |
| 5D1K Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 Deposited 2015-08-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 OXL OXALATE ION × 1 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；20% PEG-10000, 8% ethylene glycol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 1.78 Å R-free 0.202 |
| 5D1L Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A) Deposited 2015-08-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 OXL OXALATE ION × 1 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；15% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 1.62 Å R-free 0.200 |
| 5D1M Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A) Deposited 2015-08-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | OXL OXALATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；20% PEG 10000, 8% Ethylene glycol, 0.1M HEPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 1.58 Å R-free 0.223 |
| 5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
2–147（146 aa）
|
Mutation：S22R, C85K | ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2-
Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
|
Resolution 3.48 Å R-free 0.303 |
| 5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count |
Chain C
2–147（146 aa）
Chain D
2–147（146 aa）
|
Mutation：S22R, C85K Mutation：S22R, C85K | ZN ZINC ION × 16 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2-
Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
|
Resolution 3.48 Å R-free 0.303 |
| 5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain D
2–147（146 aa）
|
Mutation：S22R, C85K | ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2-
Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
|
Resolution 3.48 Å R-free 0.303 |
| 5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain I
2–147（146 aa）
|
Mutation：S22R, C85K | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2-
Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
|
Resolution 3.48 Å R-free 0.303 |
| 5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：S22R, C85K | ZN ZINC ION × 4 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
|
Resolution 2.16 Å R-free 0.231 |
| 5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain E
1–147（147 aa）
|
Mutation：S22R, C85K | ZN ZINC ION × 4 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
|
Resolution 2.16 Å R-free 0.231 |
| 5ULF Crystal Structure of a UbcH5b~Ub conjugate Deposited 2017-01-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：C21S, S22R, C85K, C107S, C111S | GOL GLYCEROL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
|
Resolution 1.80 Å R-free 0.261 |
| 5ULF Crystal Structure of a UbcH5b~Ub conjugate Deposited 2017-01-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–147（147 aa）
|
Mutation：C21S, S22R, C85K, C107S, C111S | GOL GLYCEROL × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
|
Resolution 1.80 Å R-free 0.261 |
| 5ULH Structure of RNF165 in complex with a UbcH5b~Ub conjugate Deposited 2017-01-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：C21S, C85K, C107S, C111S | GOL GLYCEROL × 2 SCN THIOCYANATE ION × 2 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；200 mM potassium thiocyanate, 20% PEG 3350
|
Resolution 1.95 Å R-free 0.217 |
| 5ULK Crystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate Deposited 2017-01-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：C21S, C85K, C107S, C111S | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；200 mM ammonium nitrate, 20% PEG 3350
|
Resolution 2.38 Å R-free 0.267 |
| 5VZW TRIM23 RING domain in complex with UbcH5-Ub Deposited 2017-05-29 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain A
1–147（147 aa）
Chain B
1–147（147 aa）
|
Mutation：S22R,C85K Mutation：S22R,C85K | ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；290 K；0.1 M Bis-Tris, pH 5.5, 0.2 M calcium chloride, 17% w/v PEG3350
|
Resolution 2.28 Å R-free 0.237 |
| 5ZBU Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub Deposited 2018-02-12 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–147（147 aa）
|
Mutation：C85K | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES monohydrate, 14% PEG 4000
|
Resolution 3.20 Å R-free 0.262 |
| 5ZBU Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub Deposited 2018-02-12 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–147（147 aa）
|
Mutation：C85K | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES monohydrate, 14% PEG 4000
|
Resolution 3.20 Å R-free 0.262 |
| 6HPR Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub Deposited 2018-09-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M ammonium fluoride and 15% (w/v) PEG 3350
|
Resolution 1.70 Å R-free 0.197 |
| 6M2C Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain Deposited 2020-02-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；4% v/v Tacsimate pH 6.0, 12% w/v Polyethylene glycol 3350
|
Resolution 2.70 Å R-free 0.258 |
| 6M2C Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain Deposited 2020-02-27 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；4% v/v Tacsimate pH 6.0, 12% w/v Polyethylene glycol 3350
|
Resolution 2.70 Å R-free 0.258 |
| 6M2C Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain Deposited 2020-02-27 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；4% v/v Tacsimate pH 6.0, 12% w/v Polyethylene glycol 3350
|
Resolution 2.70 Å R-free 0.258 |
| 6M2C Distinct mechanism of MUL1-RING domain simultaneously recruiting E2 enzyme and the substrate p53-TAD domain Deposited 2020-02-27 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；4% v/v Tacsimate pH 6.0, 12% w/v Polyethylene glycol 3350
|
Resolution 2.70 Å R-free 0.258 |
| 6SQO Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2019-09-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain B
2–147（146 aa）
Chain E
2–147（146 aa）
|
Mutation：S22R, C85K Mutation：S22R, C85K | ZN ZINC ION × 4 CL CHLORIDE ION × 4 NO3 NITRATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；292 K；0.1 M SPG, pH 7.0, 10% (w/v) PEG Smear Broad, 0.15 M NH4NO3
|
Resolution 1.41 Å R-free 0.173 |
| 6SQR Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub Deposited 2019-09-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count |
Chain B
2–147（146 aa）
Chain E
2–147（146 aa）
Chain H
2–147（146 aa）
Chain K
2–147（146 aa）
|
Mutation：S22R, C85K Mutation：S22R, C85K Mutation：S22R, C85K Mutation：S22R, C85K | 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 |
| 6SQS Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub Deposited 2019-09-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain B
2–147（146 aa）
Chain E
2–147（146 aa）
|
Mutation：S22R, C85K Mutation：S22R, C85K | ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；292 K；0.1 M Tris-HCl, pH 8.0, 15% (w/v) PEG 2000 MME and 0.1 M KCl
|
Resolution 1.83 Å R-free 0.242 |
| 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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count |
Chain D
1–147（147 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 |
| 6W7Z RNF12 RING domain in complex with Ube2d2 Deposited 2020-03-19 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | GOL GLYCEROL × 1 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；15-20% PEG 3350, 100-200 mM ammonium formate
|
Resolution 1.80 Å R-free 0.211 |
| 6W9D RNF12 RING domain in complex with a Ube2d2~Ub conjugate Deposited 2020-03-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：C21S, S22R, C85K, C107S, C111S | 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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
1–147（147 aa）
|
Mutation：C21S, S22R, C85K, C107S, C111S | 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 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain G
1–147（147 aa）
|
Mutation：C21S, S22R, C85K, C107S, C111S | 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 |
| 7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain BBB
1–147（147 aa）
|
Mutation：S22R, C85K | CL CHLORIDE ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
|
Resolution 1.56 Å R-free 0.185 |
| 7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain EEE
1–147（147 aa）
|
Mutation：S22R, C85K | CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
|
Resolution 1.56 Å R-free 0.185 |
| 7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain BBB
1–147（147 aa）
|
Mutation：S22R, C85K | CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
|
Resolution 2.07 Å R-free 0.266 |
| 7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain EEE
1–147（147 aa）
|
Mutation：S22R, C85K | CL CHLORIDE ION × 1 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
|
Resolution 2.07 Å R-free 0.266 |
| 7BOL ubiquitin-conjugating enzyme, Ube2D2 Deposited 2020-03-19 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.5 M Ammonium sulfate
0.1 M Sodium citrate pH 5.6
1.0 M Lithium sulfate
|
Resolution 1.80 Å R-free 0.219 |
| 7R71 Crystal Structure of the UbArk2C-UbcH5b~Ub complex Deposited 2021-06-24 | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–147（147 aa）
|
Mutation：C21S, S22R, C85K, C107S, C111S | 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 |
| 8B3I CRL4CSA-E2-Ub (state 2) Deposited 2022-09-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count |
Chain D
1–147（147 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 |
| 8GBQ Structure of RNF125 in complex with UbcH5b Deposited 2023-02-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | GOL GLYCEROL × 1 ZN ZINC ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9.5；289 K；0.1 M CHES 9.5
20% PEG 8000
|
Resolution 1.74 Å R-free 0.201 |
| 8GCB Structure of RNF125 in complex with a UbcH5b~Ub conjugate Deposited 2023-03-01 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
MICROBATCH；pH 9；289 K；0.1 M BICINE pH 9.0, 20% PEG 6000
|
Resolution 2.39 Å R-free 0.271 |
| 8JWJ PHD Finger Protein 7 (PHF7) in complex with UBE2D2 Deposited 2023-06-29 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–147（147 aa）
|
Mutation：S22R, C85K | ZN ZINC ION × 7 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.3；277 K；MPD, Tris
|
Resolution 2.96 Å R-free 0.222 |
| 8JWJ PHD Finger Protein 7 (PHF7) in complex with UBE2D2 Deposited 2023-06-29 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–147（147 aa）
|
Mutation：S22R, C85K | ZN ZINC ION × 7 SO4 SULFATE ION × 1 GOL GLYCEROL × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.3；277 K；MPD, Tris
|
Resolution 2.96 Å R-free 0.222 |
| 8JWU PHD Finger Protein 7 (PHF7) fused to UBE2D2 via a (GSGG)3 linker Deposited 2023-06-29 | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：S346R,C409K | ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG8000, DMSO, MOPS
|
Resolution 3.58 Å R-free 0.265 |
| 8JWU PHD Finger Protein 7 (PHF7) fused to UBE2D2 via a (GSGG)3 linker Deposited 2023-06-29 | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–147（147 aa）
|
Mutation：S346R,C409K | ZN ZINC ION × 7 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG8000, DMSO, MOPS
|
Resolution 3.58 Å R-free 0.265 |
| 8JWU PHD Finger Protein 7 (PHF7) fused to UBE2D2 via a (GSGG)3 linker Deposited 2023-06-29 | Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–147（147 aa）
|
Mutation：S346R,C409K | ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；PEG8000, DMSO, MOPS
|
Resolution 3.58 Å R-free 0.265 |
| 8V0D Ubch5B-RING3 of MIB1 fusion structure Deposited 2023-11-17 | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
Chain B
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 5 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；4% v/v TacsimateTM pH 6.0,
12% w/v Polyethylene glycol 3,350
|
Resolution 2.40 Å R-free 0.243 |
| 8VK8 Structure of UbV.d2.1 in complex with Ube2d2 Deposited 2024-01-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：C21S, C107S, and C111S | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；289 K；0.1 M Sodium citrate pH 5.6,
20% w/v PEG 4000,
20% v/v 2-Propanol
|
Resolution 2.99 Å R-free 0.295 |
| 8VK8 Structure of UbV.d2.1 in complex with Ube2d2 Deposited 2024-01-08 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
1–147（147 aa）
|
Mutation：C21S, C107S, and C111S | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；289 K；0.1 M Sodium citrate pH 5.6,
20% w/v PEG 4000,
20% v/v 2-Propanol
|
Resolution 2.99 Å R-free 0.295 |
| 8VK8 Structure of UbV.d2.1 in complex with Ube2d2 Deposited 2024-01-08 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
1–147（147 aa）
|
Mutation：C21S, C107S, and C111S | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；289 K；0.1 M Sodium citrate pH 5.6,
20% w/v PEG 4000,
20% v/v 2-Propanol
|
Resolution 2.99 Å R-free 0.295 |
| 8VK9 Structure of UbV.d2.3 in complex with Ube2d2-S22R Deposited 2024-01-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：C21S, S22R, C107S, C111S | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.1 M Sodium HEPES pH 7.0,
15% w/v PEG 20,000
|
Resolution 2.00 Å R-free 0.224 |
| 8VK9 Structure of UbV.d2.3 in complex with Ube2d2-S22R Deposited 2024-01-08 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–147（147 aa）
|
Mutation：C21S, S22R, C107S, C111S | GOL GLYCEROL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.1 M Sodium HEPES pH 7.0,
15% w/v PEG 20,000
|
Resolution 2.00 Å R-free 0.224 |
| 8VK9 Structure of UbV.d2.3 in complex with Ube2d2-S22R Deposited 2024-01-08 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
1–147（147 aa）
|
Mutation：C21S, S22R, C107S, C111S | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.1 M Sodium HEPES pH 7.0,
15% w/v PEG 20,000
|
Resolution 2.00 Å R-free 0.224 |
| 8VK9 Structure of UbV.d2.3 in complex with Ube2d2-S22R Deposited 2024-01-08 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
1–147（147 aa）
|
Mutation：C21S, S22R, C107S, C111S | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.1 M Sodium HEPES pH 7.0,
15% w/v PEG 20,000
|
Resolution 2.00 Å R-free 0.224 |
| 9DNS Cryo-EM structure of Tom1-UBE2D2-ubiquitin complex Deposited 2024-09-18 | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count |
Chain D
1–147（147 aa）
Chain E
1–147（147 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 |
| 9GLS Crystal Structure of Human UBCH5B C85E Deposited 2024-08-28 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain AAA
1–147（147 aa）
|
Mutation：C85E | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；10% PEG 200, 0.1 M Bis-Tris propane, pH 9, 15% PEG 8000
|
Resolution 1.25 Å R-free 0.211 |
| 9Q8Y Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub Deposited 2025-02-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
2–147（146 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；0.2 M Sodium acetate trihydrate, 0.1 M Imidazole pH 8.0, 10% PEG 8000
|
Resolution 2.63 Å R-free 0.275 |
| 9Q8Y Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub Deposited 2025-02-25 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
2–147（146 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；0.2 M Sodium acetate trihydrate, 0.1 M Imidazole pH 8.0, 10% PEG 8000
|
Resolution 2.63 Å R-free 0.275 |
| 9YE9 Structure of UbcH5b in complex with the U-box domain of the E3 ubiquitin ligase CHIP Deposited 2025-09-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：M1K, C85K | BME BETA-MERCAPTOETHANOL × 5 CL CHLORIDE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M Magnesium chloride hexahydrate, 0.1 M Potassium chloride, 0.1 M PIPES, 20 % v/v PEG Smear Medium
|
Resolution 2.01 Å R-free 0.288 |
| 9YEA Structure of the isopeptide bond-linked UbcH5b~Ubiquitin conjugate complex for an M1K/C85K UbcH5b mutant Deposited 2025-09-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–147（147 aa）
|
Mutation：M1K, C85K | 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 |