Current Protein Identity：P0CG47
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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 |
|---|---|---|---|---|---|---|---|
| 2MBB Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex Deposited 2013-07-29 | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
Fragment：UNP P0CG47 residues 1-76
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition
3 mM [U-100% 15N] GB1-UBM1, 3 mM [U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition
3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition
3 mM GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
|
Resolution not provided |
| 2MRO Structure of the complex of ubiquitin and the UBA domain from DNA-damage-inducible 1 protein (Ddi1) Deposited 2014-07-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：Human Ubiquitin
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.8；298.2 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition
1 mM [U-100% 15N] Ub-1, 20 mM sodium phosphate-2, 7 % [U-99% 2H] D2O-3, 93 % H2O-4, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
1 mM [U-100% 15N] UBA-5, 20 mM sodium phosphate-6, 7 % [U-99% 2H] D2O-7, 93 % H2O-8, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 2MSG Solid-state NMR structure of ubiquitin Deposited 2014-08-04 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
7–78（72 aa）
Fragment：UNP residuse 1-72
|
Not recorded | No recorded non-water small molecule | SOLID-STATE NMR |
NMR measurement conditions
273 K；Pressure ambient
NMR sample composition
20 mg [U-100% 13C; U-100% 15N] Ubiquitin, 30 mg [1-glucose 13C,U-100% 15N] Ubiquitin, 40 mg [2-glucose 13C,U-100% 15N] Ubiquitin, 40 % v/v MPD, 0.2 M CdCl2, 1 mg DSS, 100% H20 | 100% H20
|
Resolution not provided |
| 2N13 Complex structure of MyUb (1080-1122) of human Myosin VI with K63-diUb Deposited 2015-03-20 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.5；283 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition
0.5 mM [U-13C; U-15N] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2Y5B Structure of USP21 in complex with linear diubiquitin-aldehyde Deposited 2011-01-12 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–152（152 aa）
Fragment：LINEAR DIUBIQUITIN ALDEHYDE, RESIDUES 1-152
|
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 SO4 SULFATE ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；15% PEG8000, 0.2 M NH4SO4, pH 7.4
|
Resolution 2.70 Å R-free 0.279 |
| 2Y5B Structure of USP21 in complex with linear diubiquitin-aldehyde Deposited 2011-01-12 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–152（152 aa）
Fragment：LINEAR DIUBIQUITIN ALDEHYDE, RESIDUES 1-152
|
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 SO4 SULFATE ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；15% PEG8000, 0.2 M NH4SO4, pH 7.4
|
Resolution 2.70 Å R-free 0.279 |
| 3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
|
Resolution 2.70 Å R-free 0.224 |
| 3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
|
Resolution 2.70 Å R-free 0.224 |
| 3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
|
Resolution 2.70 Å R-free 0.224 |
| 3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
|
Resolution 2.70 Å R-free 0.224 |
| 3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 | Assembly 5 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric（24） Consistent with protein count |
Chain B
1–76（76 aa）
Chain D
1–76（76 aa）
Chain F
1–76（76 aa）
Chain H
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | NA SODIUM ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
|
Resolution 2.70 Å R-free 0.224 |
| 3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 | Assembly 6 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain B
1–76（76 aa）
Chain D
1–76（76 aa）
Chain F
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
|
Resolution 2.70 Å R-free 0.224 |
| 3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
|
Resolution 2.50 Å R-free 0.226 |
| 3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
|
Resolution 2.50 Å R-free 0.226 |
| 3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
|
Resolution 2.50 Å R-free 0.226 |
| 3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
|
Resolution 2.50 Å R-free 0.226 |
| 3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
|
Resolution 2.50 Å R-free 0.226 |
| 3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
|
Resolution 2.50 Å R-free 0.226 |
| 3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
|
Resolution 2.50 Å R-free 0.226 |
| 3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
|
Resolution 2.50 Å R-free 0.226 |
| 3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 | Assembly 9 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
Chain C
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
Chain D
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
|
Resolution 2.50 Å R-free 0.226 |
| 3OJ4 Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Deposited 2010-08-20 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.1；292 K；0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K
|
Resolution 3.40 Å R-free 0.319 |
| 3OJ4 Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Deposited 2010-08-20 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain E
1–76（76 aa）
Fragment：Ubiquitin, UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.1；292 K；0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K
|
Resolution 3.40 Å R-free 0.319 |
| 3ONS Crystal structure of Human Ubiquitin in a new crystal form Deposited 2010-08-30 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–72（72 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.2；277 K；2 ul of a 10 mg/ml protein solution was mixed with 2 ul of the reservoir solution (50-56 % MPD and 8-18 % (v/v) glycerol solution in 27mM sodium citrate (pH 4.0-4.2) buffer), VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.211 |
| 3PTF X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin Deposited 2010-12-02 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
Fragment：Ubiquitin
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM
TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.70 Å R-free 0.275 |
| 3PTF X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin Deposited 2010-12-02 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
Fragment：Ubiquitin
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM
TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.70 Å R-free 0.275 |
| 3ZLZ Lys6-linked tri-ubiquitin Deposited 2013-02-04 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
|
Mutation：YES Mutation：YES | ZN ZINC ION × 7 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4
|
Resolution 2.90 Å R-free 0.288 |
| 3ZLZ Lys6-linked tri-ubiquitin Deposited 2013-02-04 | Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–76（76 aa）
|
Mutation：YES | ZN ZINC ION × 6 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4
|
Resolution 2.90 Å R-free 0.288 |
| 3ZLZ Lys6-linked tri-ubiquitin Deposited 2013-02-04 | Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
|
Mutation：YES | ZN ZINC ION × 9 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.4；20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4
|
Resolution 2.90 Å R-free 0.288 |
| 3ZNH Crimean Congo Hemorrhagic Fever Virus OTU domain in complex with ubiquitin-propargyl. Deposited 2013-02-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6.5；20-30% PEG 8000, 100 MM NA CACODYLATE PH 6.5, 100 MM MG ACETATE, AND 2% N-OCTYL-BETA-D-GLUCOSIDE.
|
Resolution 2.30 Å R-free 0.275 |
| 4UEL UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain Deposited 2014-12-18 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
|
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
277 K；100 MM BIS-TRIS-PROPANE PH 5.8, 300 MM NABR, 21% PEG3350. 4 DEGREES CELSIUS
|
Resolution 2.30 Å R-free 0.234 |
| 4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
|
Resolution 3.69 Å R-free 0.269 |
| 4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain E
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
|
Resolution 3.69 Å R-free 0.269 |
| 4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain H
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
|
Resolution 3.69 Å R-free 0.269 |
| 4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain K
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
|
Resolution 3.69 Å R-free 0.269 |
| 4WHV E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B Deposited 2014-09-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：unp residues 1-76
Chain F
1–76（76 aa）
Fragment：unp residues 1-76
|
Not recorded | ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；1.04 M (NH4)2HPO4
|
Resolution 8.30 Å R-free 0.337 |
| 4WHV E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B Deposited 2014-09-23 | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain G
1–76（76 aa）
Fragment：unp residues 1-76
Chain L
1–76（76 aa）
Fragment：unp residues 1-76
|
Not recorded | ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；1.04 M (NH4)2HPO4
|
Resolution 8.30 Å R-free 0.337 |
| 4WLR Crystal Structure of mUCH37-hRPN13 CTD-hUb complex Deposited 2014-10-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.6；277 K；25% PEG 3350, 220 mM MgCl2,100 mM Bis-Tris
|
Resolution 2.00 Å R-free 0.227 |
| 4WUR The crystal structure of the MERS-CoV papain-like protease (C111S) with human ubiquitin Deposited 2014-11-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | IPA ISOPROPYL ALCOHOL × 2 ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.8；291 K；22% w/v PEG 4000, 15% v/v 2-propanol, 0.1M tri-sodium citrate pH 4.8 and 10% glycerol
|
Resolution 3.16 Å R-free 0.252 |
| 4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：UNP residues 1-76
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
|
Resolution 1.90 Å R-free 0.237 |
| 4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–76（76 aa）
Fragment：UNP residues 1-76
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
|
Resolution 1.90 Å R-free 0.237 |
| 4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–76（76 aa）
Fragment：UNP residues 1-76
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
|
Resolution 1.90 Å R-free 0.237 |
| 4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain D
1–76（76 aa）
Fragment：UNP residues 1-76
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
|
Resolution 1.90 Å R-free 0.237 |
| 4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain E
1–76（76 aa）
Fragment：UNP residues 1-76
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
|
Resolution 1.90 Å R-free 0.237 |
| 4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain F
1–76（76 aa）
Fragment：UNP residues 1-76
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
|
Resolution 1.90 Å R-free 0.237 |
| 4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 | Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain G
1–76（76 aa）
Fragment：UNP residues 1-76
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
|
Resolution 1.90 Å R-free 0.237 |
| 4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 | Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain H
1–76（76 aa）
Fragment：UNP residues 1-76
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
|
Resolution 1.90 Å R-free 0.237 |
| 4XOF Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin crystals without Zinc. Deposited 2015-01-16 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0
|
Resolution 1.15 Å R-free 0.171 |
| 4ZFR Catalytic domain of Sst2 F403A mutant bound to ubiquitin Deposited 2015-04-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
77–152（76 aa）
Fragment：unp residues 77-152
|
Not recorded | ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2M sodium citrate tribasic diehydrate, 0.1M HEPES sodium, 20% v/v 2-propanol
|
Resolution 1.72 Å R-free 0.237 |
| 4ZFT Catalytic domain of Sst2 F403W mutant bound to ubiquitin Deposited 2015-04-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
77–152（76 aa）
Fragment：unp residues 77-152
|
Not recorded | ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；(0.04 M Citric acid, 0.06 M BIS-TRIS propane), 20% w/v PEG 3,350
|
Resolution 2.30 Å R-free 0.235 |
| 4ZFT Catalytic domain of Sst2 F403W mutant bound to ubiquitin Deposited 2015-04-21 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
77–152（76 aa）
Fragment：unp residues 77-152
|
Not recorded | ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；(0.04 M Citric acid, 0.06 M BIS-TRIS propane), 20% w/v PEG 3,350
|
Resolution 2.30 Å R-free 0.235 |
| 4ZPZ Crystal Structure of Semi-synthetic Ubiquitin with Phospho-Ser65 and Ala46Cys Deposited 2015-05-08 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–73（73 aa）
Fragment：ubiquitin, UNP residues 1-73
Chain B
1–73（73 aa）
Fragment：ubiquitin, UNP residues 1-73
|
Mutation：A46C, Phospho-Ser65 Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：A46C, Phospho-Ser65 Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；50 mM sodium cacodylate, 25% PEG 4000
|
Resolution 1.54 Å R-free 0.173 |
| 4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain X
1–76（76 aa）
Chain c
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 16 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
|
Resolution 3.82 Å R-free 0.256 |
| 4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 | Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain h
1–76（76 aa）
Chain m
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 16 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
|
Resolution 3.82 Å R-free 0.256 |
| 5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
|
Resolution 2.49 Å R-free 0.304 |
| 5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain I
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
|
Resolution 2.49 Å R-free 0.304 |
| 5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
|
Resolution 2.49 Å R-free 0.304 |
| 5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
|
Resolution 2.49 Å R-free 0.304 |
| 5CAW Structure of Pediculus humanus Parkin bound to phospho-ubiquitin Deposited 2015-06-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Mutation：G76 exchanged to chemical probe Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 8 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；2% (v/v) PEG400, 2 M NH4SO4, 0.1 M HEPES pH 7.5
|
Resolution 2.62 Å R-free 0.260 |
| 5CAW Structure of Pediculus humanus Parkin bound to phospho-ubiquitin Deposited 2015-06-30 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Mutation：G76 exchanged to chemical probe Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 8 SO4 SULFATE ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；2% (v/v) PEG400, 2 M NH4SO4, 0.1 M HEPES pH 7.5
|
Resolution 2.62 Å R-free 0.260 |
| 5CRA Structure of the SdeA DUB Domain Deposited 2015-07-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–75（75 aa）
Fragment：UNP residues 1-75
|
Not recorded | SO4 SULFATE ION × 6 GVE METHYL 4-AMINOBUTANOATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris:HCl, 3.0 M Sodium Chloride
|
Resolution 2.64 Å R-free 0.236 |
| 5CRA Structure of the SdeA DUB Domain Deposited 2015-07-22 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–75（75 aa）
Fragment：UNP residues 1-75
|
Not recorded | SO4 SULFATE ION × 3 GVE METHYL 4-AMINOBUTANOATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris:HCl, 3.0 M Sodium Chloride
|
Resolution 2.64 Å R-free 0.236 |
| 5CVM USP46~ubiquitin BEA covalent complex Deposited 2015-07-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–59（59 aa）
Fragment：UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；292 K；3.6 M sodium formate
|
Resolution 1.90 Å R-free 0.197 |
| 5CVN WDR48 (2-580):USP46~ubiquitin ternary complex Deposited 2015-07-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.8；292 K；0.1 M sodium chloride, 5% ethanol, 15% MPD, 0.1 M Tris pH 8.8
|
Resolution 3.36 Å R-free 0.222 |
| 5CVO WDR48:USP46~ubiquitin ternary complex Deposited 2015-07-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；15% MPD, 0.1 M NaCl, 0.1 M HEPES, pH 7.0
|
Resolution 3.88 Å R-free 0.275 |
| 5CVO WDR48:USP46~ubiquitin ternary complex Deposited 2015-07-27 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain F
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；15% MPD, 0.1 M NaCl, 0.1 M HEPES, pH 7.0
|
Resolution 3.88 Å R-free 0.275 |
| 5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
|
Resolution 2.65 Å R-free 0.238 |
| 5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain E
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
|
Resolution 2.65 Å R-free 0.238 |
| 5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain H
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
|
Resolution 2.65 Å R-free 0.238 |
| 5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain K
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
|
Resolution 2.65 Å R-free 0.238 |
| 5D0M Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | PO4 PHOSPHATE ION × 1 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；SPG buffer, PEG 1500
|
Resolution 1.91 Å R-free 0.213 |
| 5DFL Crystal structure of Ube2K~Ubiquitin conjugate Deposited 2015-08-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M di-ammonium citrate pH 5.0, 20% PEG 3350
|
Resolution 2.10 Å R-free 0.235 |
| 5DK8 Human ubiquitin in the P1 space group Deposited 2015-09-03 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–75（74 aa）
Fragment：Ubiquitin, UNP residues 2-75
|
Not recorded | MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；288 K；0.2M magnesium chloride hexahydrate, 30% w/v PEG 4000, 0.1 M Tris pH 8.5
|
Resolution 1.32 Å R-free 0.201 |
| 5DK8 Human ubiquitin in the P1 space group Deposited 2015-09-03 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
2–75（74 aa）
Fragment：Ubiquitin, UNP residues 2-75
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；288 K；0.2M magnesium chloride hexahydrate, 30% w/v PEG 4000, 0.1 M Tris pH 8.5
|
Resolution 1.32 Å R-free 0.201 |
| 5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–75（75 aa）
|
Not recorded | ACT ACETATE ION × 1 NI NICKEL (II) ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
|
Resolution 2.85 Å R-free 0.264 |
| 5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain F
1–75（75 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
|
Resolution 2.85 Å R-free 0.264 |
| 5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain E
1–76（76 aa）
Fragment：UNP residues 1-76
Chain G
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2-
Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
|
Resolution 3.48 Å R-free 0.303 |
| 5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count |
Chain E
1–76（76 aa）
Fragment：UNP residues 1-76
Chain F
1–76（76 aa）
Fragment：UNP residues 1-76
Chain G
1–76（76 aa）
Fragment：UNP residues 1-76
Chain H
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | ZN ZINC ION × 16 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2-
Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
|
Resolution 3.48 Å R-free 0.303 |
| 5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain F
1–76（76 aa）
Fragment：UNP residues 1-76
Chain H
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2-
Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
|
Resolution 3.48 Å R-free 0.303 |
| 5EMZ Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit Deposited 2015-11-07 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
|
Mutation：F45W | SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；LiSO
Tris
PEG-3350
|
Resolution 1.66 Å R-free 0.209 |
| 5EMZ Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit Deposited 2015-11-07 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
|
Mutation：F45W | SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；LiSO
Tris
PEG-3350
|
Resolution 1.66 Å R-free 0.209 |
| 5EMZ Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit Deposited 2015-11-07 | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
1–76（76 aa）
Chain F
1–76（76 aa）
|
Mutation：F45W | SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；LiSO
Tris
PEG-3350
|
Resolution 1.66 Å R-free 0.209 |
| 5EYA TRIM25 RING domain in complex with Ubc13-Ub conjugate Deposited 2015-11-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain C
1–76（76 aa）
Fragment：UNP residues 1-76
Chain D
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Li citrate, 20% PEG 3350
|
Resolution 2.40 Å R-free 0.228 |
| 5GJQ Structure of the human 26S proteasome bound to USP14-UbAl Deposited 2016-07-01 | Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric（48） Consistent with protein count |
Chain y
1–76（76 aa）
Fragment：UNP RESIDUES 1-76
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ADP ADENOSINE-5'-DIPHOSPHATE × 6 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2 seconds before plunging
|
Resolution 4.35 Å |
| 5GO7 Linear tri-ubiquitin Deposited 2016-07-26 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；0.2M sodium dihydrogen phosphate, 20% PEG 3350, PH 6.0
|
Resolution 1.80 Å R-free 0.310 |
| 5GO8 Linear tetra-ubiquitin Deposited 2016-07-26 | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；0.2M Sodium acetate trihydrate, 20% PEG 3350, PH8.0
|
Resolution 2.21 Å R-free 0.322 |
| 5GOB Lys6-linked di-ubiquitin Deposited 2016-07-26 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.9；289 K；0.2M Magnesium chloride hexahydrate, 20% PEG 3350, PH5.9
|
Resolution 1.15 Å R-free 0.229 |
| 5GOC Lys11-linked diubiquitin Deposited 2016-07-26 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Li2SO4, 0.1M tris 8.5, 30% PEG 4000
|
Resolution 1.73 Å R-free 0.235 |
| 5GOD Lys27-linked di-ubiquitin Deposited 2016-07-26 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium acetate tetrahydrate, 0.1M Sodium cacodylate trihydrate PH6.5, 20% PEG 8000
|
Resolution 1.15 Å R-free 0.222 |
| 5GOG Lys29-linked di-ubiquitin Deposited 2016-07-27 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Potassium sulfate, 20% PEG 3350
|
Resolution 1.98 Å R-free 0.330 |
| 5GOH Lys33-linked di-ubiquitin Deposited 2016-07-27 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium sulfate heptahydrate, 20% peg 3350
|
Resolution 1.95 Å R-free 0.271 |
| 5GOI Lys48-linked di-ubiquitin Deposited 2016-07-27 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.1M Sodium citrate tribasic dehydrate PH5.6, 20% 2-Propanol, 20%PEG 4000
|
Resolution 1.59 Å R-free 0.311 |
| 5GOJ Lys63-linked di-ubiquitin Deposited 2016-07-27 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.1M TRIS hydrochloride PH8.5, 2.0M Ammonium phosphate monobasic
|
Resolution 1.55 Å R-free 0.253 |
| 5GOK K11/K63-branched tri-Ubiquitin Deposited 2016-07-27 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；0.2M MgSO4, 20% PEG 3350, 4mM CdCl2, PH6.0
|
Resolution 1.84 Å R-free 0.245 |
| 5H7S Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain Deposited 2016-11-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain E
1–76（76 aa）
Chain F
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；0.04 M Citric acid, 0.06 M BIS-TRIS propane, pH 6.4, 20% w/v polyethylene glycol 3350
|
Resolution 3.49 Å R-free 0.286 |
| 5IBK Skp1-F-box in complex with a ubiquitin variant Deposited 2016-02-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
75–150（76 aa）
Fragment：UNP residues 75-150
|
Mutation：L8G, T9A, G10R, K11T, T12A, R42I, A46S, G47R, Q49L, Q62H, K63R, H68R, R72I, L73F | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol
|
Resolution 2.50 Å R-free 0.240 |
| 5IBK Skp1-F-box in complex with a ubiquitin variant Deposited 2016-02-22 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain F
75–150（76 aa）
Fragment：UNP residues 75-150
|
Mutation：L8G, T9A, G10R, K11T, T12A, R42I, A46S, G47R, Q49L, Q62H, K63R, H68R, R72I, L73F | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol
|
Resolution 2.50 Å R-free 0.240 |
| 5IFR Structure of the stable UBE2D3-UbDha conjugate Deposited 2016-02-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；200mM tripotassium citrate, 20% PEG 3350
|
Resolution 2.20 Å R-free 0.243 |
| 5J8P Lys27-linked diubiquitin Deposited 2016-04-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.2M magnesium acetate tetrahydrate, 0.1M sodium cacodylate trihydrate, pH 6.5, 20% PEG 8000
|
Resolution 1.55 Å R-free 0.295 |
| 5JBV Lys27-linked triubiquitin Deposited 2016-04-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | NO3 NITRATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.9；291 K；20% (w/v) PEG 3350, 4mM CdCl2, pH 5.9, 200mM Mg(NO3)2
|
Resolution 2.10 Å R-free 0.306 |
| 5JBY Lys27-linked triubiquitin Deposited 2016-04-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain A
1–76（76 aa）
Chain C
1–76（76 aa）
Chain E
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% (w/v) PEG 3350, 4mM CdCl2, pH 5.9, 200mM Mg(NO3)2
|
Resolution 1.99 Å R-free 0.308 |
| 5JG6 APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C Deposited 2016-04-19 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
76–154（79 aa）
|
Not recorded | ZN ZINC ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4.6, 33% PEG4000
|
Resolution 2.00 Å R-free 0.220 |
| 5JG6 APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C Deposited 2016-04-19 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
76–154（79 aa）
|
Not recorded | ZN ZINC ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4.6, 33% PEG4000
|
Resolution 2.00 Å R-free 0.220 |
| 5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M CHES (pH 9.5)
1.0M sodium citrate
|
Resolution 2.90 Å R-free 0.285 |
| 5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M CHES (pH 9.5)
1.0M sodium citrate
|
Resolution 2.90 Å R-free 0.285 |
| 5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M CHES (pH 9.5)
1.0M sodium citrate
|
Resolution 2.90 Å R-free 0.285 |
| 5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M CHES (pH 9.5)
1.0M sodium citrate
|
Resolution 2.90 Å R-free 0.285 |
| 5JTJ USP7CD-CTP in complex with Ubiquitin Deposited 2016-05-09 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | CA CALCIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.05 M Calcium chloride, 0.1 M MES pH 6.0 and 45% PEG 200
|
Resolution 3.32 Å R-free 0.209 |
| 5JTJ USP7CD-CTP in complex with Ubiquitin Deposited 2016-05-09 | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | CA CALCIUM ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.05 M Calcium chloride, 0.1 M MES pH 6.0 and 45% PEG 200
|
Resolution 3.32 Å R-free 0.209 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
1–76（76 aa）
Chain F
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count |
Chain B
1–76（76 aa）
Chain D
1–76（76 aa）
Chain F
1–76（76 aa）
Chain H
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 | Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain D
1–76（76 aa）
Chain H
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
|
Resolution 3.31 Å R-free 0.269 |
| 5K9P Ser20 phosphorylated ubiquitin Deposited 2016-06-01 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；45% (w/v) PEG 400, 100 mM tris-HCl
|
Resolution 1.55 Å R-free 0.219 |
| 5KGF Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution Deposited 2016-06-13 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain M
1–76（76 aa）
Chain O
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；High concentration NCP-ubme/GST-53BP1 complex at 200 mM salt was diluted just prior to grid freezing.
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE；Plunged into liquid ethane-propane (FEI VITROBOT MARK III)
|
Resolution 4.54 Å |
| 5KHY Crystal structure of oxime-linked K6 diubiquitin Deposited 2016-06-16 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–73（73 aa）
Chain B
1–75（75 aa）
|
Mutation：Unnatural aminoxylysine amino acid at position 6 Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：unnatural residue 76 oxime linked to chain A | ZN ZINC ION × 10 ETA ETHANOLAMINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 3350, Zinc acetate
|
Resolution 3.50 Å R-free 0.331 |
| 5KYC Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin (malonate bound) Deposited 2016-07-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | MLA MALONIC ACID × 1 GOL GLYCEROL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；8% tacsimate pH 4.0, 20% PEG3350
|
Resolution 1.43 Å R-free 0.192 |
| 5KYD Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin Deposited 2016-07-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；0.2M Ammonium fluoride, 20% PEG3350
|
Resolution 1.62 Å R-free 0.213 |
| 5KYE Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin Deposited 2016-07-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350, 0.2M Ammonium acetate
|
Resolution 1.97 Å R-free 0.223 |
| 5KYE Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin Deposited 2016-07-21 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350, 0.2M Ammonium acetate
|
Resolution 1.97 Å R-free 0.223 |
| 5KYF Crystal structure of USP7 catalytic domain [L299A] mutant in complex with ubiquitin Deposited 2016-07-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | GOL GLYCEROL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350
|
Resolution 1.45 Å R-free 0.185 |
| 5L8H Structure of USP46-UbVME Deposited 2016-06-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.96M Sodium Citrate pH7.5 and 0.1mM zinc chloride
Cryo - 20% Glycerol
|
Resolution 1.85 Å R-free 0.194 |
| 5L8W Structure of USP12-UB-PRG/UAF1 Deposited 2016-06-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 GOL GLYCEROL × 1 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；3.2% PEG4000, 0.1mM MMT pH6.5, 0.1 mM TCEP.
Cryo- 30% Glycerol
|
Resolution 2.79 Å R-free 0.259 |
| 5L9T Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with E2 UBE2S poised for polyubiquitination where UBE2S, APC2, and APC11 are modeled into low resolution density Deposited 2016-06-11 | Assembly 1 Insufficient information Heteromer；Protein × 22 PDB declaration: 22-meric（22） Consistent with protein count |
Chain S
77–153（77 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.40 Å |
| 5LN1 STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST; Deposited 2016-08-02 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain U
77–152（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
EVAPORATION, RECRYSTALLIZATION；pH 6.5；292 K；12% (W/V) PEG 20000, 0.1M MES PH 6.5,
VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K
|
Resolution 3.14 Å R-free 0.248 |
| 5LRV Structure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diubiquitin Deposited 2016-08-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
Chain C
1–75（75 aa）
|
Mutation：K11X Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) | PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M phosphate citrate (pH 4.2), 20% (w/v) PEG 8K, 0.2 M sodium chloride
|
Resolution 2.80 Å R-free 0.244 |
| 5LRW Structure of Cezanne/OTUD7B OTU domain bound to ubiquitin Deposited 2016-08-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium acetate (pH 4.8), 6% (w/v) PEG 6K
|
Resolution 2.00 Å R-free 0.217 |
| 5LRW Structure of Cezanne/OTUD7B OTU domain bound to ubiquitin Deposited 2016-08-22 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–75（75 aa）
|
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium acetate (pH 4.8), 6% (w/v) PEG 6K
|
Resolution 2.00 Å R-free 0.217 |
| 5LRX Structure of A20 OTU domain bound to ubiquitin Deposited 2016-08-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；287 K；0.1 M MES/imidazole (pH 6.5), 7% (w/v) PEG 8K, 20% ethylene glycol
|
Resolution 2.85 Å R-free 0.246 |
| 5LRX Structure of A20 OTU domain bound to ubiquitin Deposited 2016-08-22 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；287 K；0.1 M MES/imidazole (pH 6.5), 7% (w/v) PEG 8K, 20% ethylene glycol
|
Resolution 2.85 Å R-free 0.246 |
| 5M93 Crystal structure of SdeA-modified ubiquitin. Deposited 2016-10-31 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
76–152（77 aa）
|
Mutation：M1S | SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
|
Resolution 1.79 Å R-free 0.231 |
| 5M93 Crystal structure of SdeA-modified ubiquitin. Deposited 2016-10-31 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
76–152（77 aa）
|
Mutation：M1S | SO4 SULFATE ION × 1 RIB alpha-D-ribofuranose × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
|
Resolution 1.79 Å R-free 0.231 |
| 5M93 Crystal structure of SdeA-modified ubiquitin. Deposited 2016-10-31 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
76–152（77 aa）
|
Mutation：M1S | RIB alpha-D-ribofuranose × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
|
Resolution 1.79 Å R-free 0.231 |
| 5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
77–152（76 aa）
|
Not recorded | ZN ZINC ION × 4 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
|
Resolution 2.16 Å R-free 0.231 |
| 5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain F
77–152（76 aa）
|
Not recorded | ZN ZINC ION × 4 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
|
Resolution 2.16 Å R-free 0.231 |
| 5N2W WT-Parkin and pUB complex Deposited 2017-02-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 8 CL CHLORIDE ION × 1 TMO trimethylamine oxide × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；100mM Tris pH 8.5, 200mM TMAO, PEG MME 2000
|
Resolution 2.68 Å R-free 0.243 |
| 5N38 S65DParkin and pUB complex Deposited 2017-02-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；100mM Tris pH 8.5, 200mM TMAO, PEG MME 2000
|
Resolution 2.60 Å R-free 0.236 |
| 5NL5 Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–76（76 aa）
|
Mutation：E16V | ZN ZINC ION × 3 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2
|
Resolution 1.96 Å R-free 0.237 |
| 5NL5 Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–76（76 aa）
|
Mutation：E16V | ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2
|
Resolution 1.96 Å R-free 0.237 |
| 5NL5 Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–76（76 aa）
|
Mutation：E16V | ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2
|
Resolution 1.96 Å R-free 0.237 |
| 5NLJ Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–76（76 aa）
|
Mutation：E16V | ACT ACETATE ION × 4 ZN ZINC ION × 5 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 70 mM Zn(CH3COO)2 and 20% v/v TFE.
|
Resolution 1.53 Å R-free 0.240 |
| 5NLJ Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–76（76 aa）
|
Mutation：E16V | ACT ACETATE ION × 1 ZN ZINC ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 ETF TRIFLUOROETHANOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 70 mM Zn(CH3COO)2 and 20% v/v TFE.
|
Resolution 1.53 Å R-free 0.240 |
| 5NLJ Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–76（76 aa）
|
Mutation：E16V | ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 70 mM Zn(CH3COO)2 and 20% v/v TFE.
|
Resolution 1.53 Å R-free 0.240 |
| 5NVG Thr12 Phosphorylated Ubiquitin Deposited 2017-05-04 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.2；291.15 K；20% (v/v) ethanol, 20% (w/v) PEG-1000, 0.1M Phosphate-citrate pH 4.2
|
Resolution 1.07 Å R-free 0.167 |
| 5O44 Crystal structure of unbranched mixed tri-Ubiquitin chain containing K48 and K63 linkages. Deposited 2017-05-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count |
Chain B
1–74（74 aa）
Chain C
1–74（74 aa）
Chain D
1–76（76 aa）
Chain F
1–76（76 aa）
|
Mutation：Deleted for Gly 75 and Gly 76 Mutation：Deleted for Gly 75 and Gly 76 Mutation：K48R Mutation：K48R | SO4 SULFATE ION × 18 MG MAGNESIUM ION × 6 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.3M MgSo4 and 100mM MES monohydrate pH 6.5
|
Resolution 3.14 Å R-free 0.254 |
| 5O6T BIRC4 RING in complex with dimeric ubiquitin variant Deposited 2017-06-07 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
75–150（76 aa）
Chain D
75–150（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；291 K；0.1 M NaHEPES pH 7.5, 1.4 M tri-Na citrate
|
Resolution 1.57 Å R-free 0.183 |
| 5OHK Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (high resolution) Deposited 2017-07-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.4；291 K；10% (w/v) PEG 20000, 0.1 M sodium citrate pH 5.4, 0.2 M lithium sulfate
|
Resolution 2.34 Å R-free 0.261 |
| 5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain J
1–76（76 aa）
Chain K
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME
200mM Ammonium Acetate
0.1M Tris pH 8.5
|
Resolution 2.50 Å R-free 0.227 |
| 5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain J
1–76（76 aa）
Chain K
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME
200mM Ammonium Acetate
0.1M Tris pH 8.5
|
Resolution 2.50 Å R-free 0.227 |
| 5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain L
1–76（76 aa）
Chain N
1–76（76 aa）
|
Not recorded | 15P POLYETHYLENE GLYCOL (N=34) × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME
200mM Ammonium Acetate
0.1M Tris pH 8.5
|
Resolution 2.50 Å R-free 0.227 |
| 5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain L
1–76（76 aa）
Chain N
1–76（76 aa）
|
Not recorded | 15P POLYETHYLENE GLYCOL (N=34) × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME
200mM Ammonium Acetate
0.1M Tris pH 8.5
|
Resolution 2.50 Å R-free 0.227 |
| 5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain I
1–76（76 aa）
Chain M
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME
200mM Ammonium Acetate
0.1M Tris pH 8.5
|
Resolution 2.50 Å R-free 0.227 |
| 5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 | Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain I
1–76（76 aa）
Chain M
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME
200mM Ammonium Acetate
0.1M Tris pH 8.5
|
Resolution 2.50 Å R-free 0.227 |
| 5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 | Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain O
1–76（76 aa）
Chain P
1–76（76 aa）
|
Not recorded | 15P POLYETHYLENE GLYCOL (N=34) × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME
200mM Ammonium Acetate
0.1M Tris pH 8.5
|
Resolution 2.50 Å R-free 0.227 |
| 5OHN Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution) Deposited 2017-07-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% (w/v) PAA 5100 Na, 100 mM Hepes pH 8.0, 2.5% (v/v) glycerol
|
Resolution 3.60 Å R-free 0.253 |
| 5OHN Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution) Deposited 2017-07-17 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% (w/v) PAA 5100 Na, 100 mM Hepes pH 8.0, 2.5% (v/v) glycerol
|
Resolution 3.60 Å R-free 0.253 |
| 5OHP Crystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin Deposited 2017-07-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.73 M sodium citrate, 0.1 M Hepes pH 7.0
|
Resolution 2.80 Å R-free 0.249 |
| 5TOF Room temperature structure of ubiquitin variant u7ub25 Deposited 2016-10-17 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
75–152（78 aa）
|
Not recorded | SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1ul protein solution at 20 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.6, 2.6 M ammonium sulfate)
|
Resolution 1.12 Å R-free 0.175 |
| 5TOG Room temperature structure of ubiquitin variant u7ub25.2540 Deposited 2016-10-17 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
75–152（78 aa）
|
Not recorded | SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1ul protein solution at 10 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.2, 2.2 M ammonium sulfate)
|
Resolution 1.08 Å R-free 0.121 |
| 5TOG Room temperature structure of ubiquitin variant u7ub25.2540 Deposited 2016-10-17 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
75–152（78 aa）
|
Not recorded | SO4 SULFATE ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1ul protein solution at 10 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.2, 2.2 M ammonium sulfate)
|
Resolution 1.08 Å R-free 0.121 |
| 5TUT UbcH5a-Ub isopeptide conjugate Deposited 2016-11-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；Hampton PEG/Ion F10
|
Resolution 2.60 Å R-free 0.243 |
| 5UJL Representative 1-conformer ensembles of K27-linked Ub2 from RDC data Deposited 2017-01-18 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：residues 1-76
Chain B
1–76（76 aa）
Fragment：residues 1-76
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.8；296 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR measurement conditions
pH 6.8；296 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition
150 uM [U-99% 15N] K27-diubiquitin, Distal Ub is 15N-labelled Proximal Ub is not enriched, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
150 uM [U-99% 15N] K27-diubiquitin, Distal Ub is not enriched Proximal Ub is 15N-labelled, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 5UJN Representative 2-conformer ensembles of K27-linked Ub2 from RDC data Deposited 2017-01-18 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.8；296 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition
150 uM [U-99% 15N] distal K27-Ub2, 20 mM NaPhosphate, 0.02 % NaN3, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
150 uM [U-99% 15N] proximal K27-Ub2, 20 mM NaPhosphate, 0.02 % NaN3, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 5ULF Crystal Structure of a UbcH5b~Ub conjugate Deposited 2017-01-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
|
Resolution 1.80 Å R-free 0.261 |
| 5ULF Crystal Structure of a UbcH5b~Ub conjugate Deposited 2017-01-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
|
Resolution 1.80 Å R-free 0.261 |
| 5ULH Structure of RNF165 in complex with a UbcH5b~Ub conjugate Deposited 2017-01-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 2 SCN THIOCYANATE ION × 2 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；200 mM potassium thiocyanate, 20% PEG 3350
|
Resolution 1.95 Å R-free 0.217 |
| 5ULK Crystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate Deposited 2017-01-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；200 mM ammonium nitrate, 20% PEG 3350
|
Resolution 2.38 Å R-free 0.267 |
| 5V1Y Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex Deposited 2017-03-02 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.8；277 K；0.1 M citric acid, pH 4.6, 20% PEG6000
|
Resolution 1.42 Å R-free 0.175 |
| 5V1Y Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex Deposited 2017-03-02 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.8；277 K；0.1 M citric acid, pH 4.6, 20% PEG6000
|
Resolution 1.42 Å R-free 0.175 |
| 5V1Z Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex Deposited 2017-03-02 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M sodium acetate, pH 4.6, 22.5% PEG3350
|
Resolution 2.00 Å R-free 0.182 |
| 5V1Z Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex Deposited 2017-03-02 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M sodium acetate, pH 4.6, 22.5% PEG3350
|
Resolution 2.00 Å R-free 0.182 |
| 5VEY Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A Lys15 in complex with RNF169 (653-708) Deposited 2017-04-06 | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6；303 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR measurement conditions
pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
NMR sample composition
90% H2O/10% D2O
|
Resolution not provided |
| 5VF0 Solution NMR structure of human RAD18 (198-240) in complex with ubiquitin Deposited 2017-04-06 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 | SOLUTION NMR |
NMR measurement conditions
pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR sample composition
0.6 mM [U-100% 13C; U-100% 15N] RAD18, 3 mM Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
3 mM RAD18, 0.6 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.9 mM [U-15N] RAD18, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.9 mM [U-100% 13C; U-100% 15N] RAD18, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.2 mM [U-100% 15N] RAD18, 1.0 mM Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 5 % Alkyl-polyethylene glycol (C12E5)/n-hexanol mixture, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.0 mM RAD18, 0.2 mM [U-100% 15N] Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 5 % Alkyl-polyethylene glycol (C12E5)/n-hexanol mixture, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 5VNZ Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 6 | X-RAY DIFFRACTION |
X-ray crystallization conditions
MICROBATCH；289 K；0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350
|
Resolution 3.41 Å R-free 0.294 |
| 5VNZ Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01 | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain F
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 6 | X-RAY DIFFRACTION |
X-ray crystallization conditions
MICROBATCH；289 K；0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350
|
Resolution 3.41 Å R-free 0.294 |
| 5VO0 Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain C
1–76（76 aa）
Chain F
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 8 K POTASSIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；100-200 mM Na/K tartrate, 11-15% PEG 3350 and 100 mM bis-Tris propane pH 7.5
|
Resolution 3.90 Å R-free 0.299 |
| 5VZM Solution NMR structure of human Rev1 (932-1039) in complex with ubiquitin Deposited 2017-05-29 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 7；303 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate；Pressure 1
NMR measurement conditions
pH 6.8；303 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate；Pressure 1
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] Ubiquitin, 20 mM Sodium phosphate buffer, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] Rev1, 3 mM Ubiquitin, 50 mM Sodium phosphate buffer, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
3 mM Rev1, 1 mM [U-100% 13C; U-100% 15N] Ubiquitin, 50 mM Sodium phosphate buffer, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 5VZW TRIM23 RING domain in complex with UbcH5-Ub Deposited 2017-05-29 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；290 K；0.1 M Bis-Tris, pH 5.5, 0.2 M calcium chloride, 17% w/v PEG3350
|
Resolution 2.28 Å R-free 0.237 |
| 5W46 Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution Deposited 2017-06-09 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–76（76 aa）
|
Mutation：S65D | MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；295 K；Tris pH 8.0, magnesium chloride, PEG 3350, Hepes
|
Resolution 1.18 Å R-free 0.190 |
| 5W46 Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution Deposited 2017-06-09 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–76（76 aa）
|
Mutation：S65D | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；295 K；Tris pH 8.0, magnesium chloride, PEG 3350, Hepes
|
Resolution 1.18 Å R-free 0.190 |
| 5WFI X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin Deposited 2017-07-12 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 5 FMT FORMIC ACID × 1 ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；50 mM Tris, pH 7.5, 100 mM sodium chloride, 5 mM DTT, 0.2 M potassium formate, 20% PEG3350
|
Resolution 1.85 Å R-free 0.197 |
| 5WFI X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin Deposited 2017-07-12 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 5 FMT FORMIC ACID × 1 ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；50 mM Tris, pH 7.5, 100 mM sodium chloride, 5 mM DTT, 0.2 M potassium formate, 20% PEG3350
|
Resolution 1.85 Å R-free 0.197 |
| 5X3M crystal structure of p-Ub-S65-NH2 Deposited 2017-02-06 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Lithium Sulfate monohydrate, 0.1M HEPES pH 7.5, 25%(w/v) Polyethylene Glycol 3350
|
Resolution 1.82 Å R-free 0.271 |
| 5X3N Crystal structure of DiUb-K6 Deposited 2017-02-06 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | PO4 PHOSPHATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium formate dihydrate, 20%(w/v) Polyethylene glycol 3350
|
Resolution 1.65 Å R-free 0.276 |
| 5X3O Crystal structure of p-DiUb-S65-COOH Deposited 2017-02-06 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：UNP residues 1-76
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Ammonium phosphate monobasic, 20%(w/v) Polyethylene glycol 3350
|
Resolution 2.19 Å R-free 0.315 |
| 5XBO Lanthanoid tagging via an unnatural amino acid for protein structure characterization Deposited 2017-03-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：UNP residues 1-76
|
Not recorded | TB TERBIUM(III) ION × 1 | SOLUTION NMR |
NMR measurement conditions
pH 7.2；298 K；Ionic strength (raw mmCIF value) 100；Pressure 760
NMR sample composition
20mM HEPES, 100mM sodium chloride, 10% D2O, 0.2mM [U-99% 15N] ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
20mM HEPES, 100mM sodium chloride, 0.1mM [U-99% 15N] HHR23A UBA1 Domain, 0.1 mM ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 5XDP K11/48-branched teraubiquitin Deposited 2017-03-28 | Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；289 K；0.2M Potassium nitrate, 20% w/v Polyethylene glycol 3350
|
Resolution 2.38 Å R-free 0.271 |
| 5XK4 Retracted state of S65-phosphorylated ubiquitin Deposited 2017-05-05 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：UNP residues 1-76
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition
0.8 mM [U-98% 13C; U-98% 15N] phosphorylated ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 5XK5 Relaxed state of S65-phosphorylated ubiquitin Deposited 2017-05-05 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：UNP residues 1-76
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition
0.8 mM [U-98% 13C; U-98% 15N] relaxed pUb, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 5XPK Crystal structure of ubiquitin-k6mimic Deposited 2017-06-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Ammonium formate, 20% w/v PEG 3350
|
Resolution 2.27 Å R-free 0.310 |
| 5YIJ Structure of a Legionella effector with substrates Deposited 2017-10-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
1–76（76 aa）
Fragment：UNP RESIDUES 1-76
Chain D
1–76（76 aa）
Fragment：UNP RESIDUES 1-76
Chain G
1–76（76 aa）
Fragment：UNP RESIDUES 1-76
|
Not recorded | NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；PEG 1000, Tris
|
Resolution 3.18 Å R-free 0.275 |
| 5YIK Structure of a Legionella effector with its substrate Deposited 2017-10-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
1–76（76 aa）
Fragment：UNP RESIDUES 1-76
Chain D
1–76（76 aa）
Fragment：UNP RESIDUES 1-76
Chain F
1–76（76 aa）
Fragment：UNP RESIDUES 1-76
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；PEG 1000, Tris
|
Resolution 3.10 Å R-free 0.279 |
| 5YMY The structure of the complex between Rpn13 and K48-diUb Deposited 2017-10-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
|
Mutation：K48R | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition
0.58 mM [U-13C; U-15N; U-2H] Rpn13, 20 mM MES, 0.15 M sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
77–152（76 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
|
Resolution 1.50 Å R-free 0.225 |
| 5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
77–152（76 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
|
Resolution 1.50 Å R-free 0.225 |
| 5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
77–152（76 aa）
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
|
Resolution 1.50 Å R-free 0.225 |
| 5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
77–152（76 aa）
|
Not recorded | ZN ZINC ION × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
|
Resolution 1.50 Å R-free 0.225 |
| 5ZBU Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub Deposited 2018-02-12 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain E
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES monohydrate, 14% PEG 4000
|
Resolution 3.20 Å R-free 0.262 |
| 5ZD0 Solution structure of human ubiquitin with three alanine mutations in living eukaryotic cells by in-cell NMR spectroscopy Deposited 2018-02-22 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–76（76 aa）
|
Mutation：L8A,I44A,V70A | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 0；300 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR measurement conditions
pH 0；300 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR sample composition
50 uM [U-100% 13C; U-100% 15N] human ubiquitin with three alanine mutations 1, 50 uM [U-100% 15N] human ubiquitin with three alanine mutations 2, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
Fragment：UNP residues 1-76
|
Mutation：K48R | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
|
Resolution 2.60 Å R-free 0.236 |
| 6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
Fragment：UNP residues 1-76
|
Mutation：K48R | GOL GLYCEROL × 1 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
|
Resolution 2.60 Å R-free 0.236 |
| 6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–77（77 aa）
Fragment：UNP residues 1-77
|
Mutation：M77D | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
|
Resolution 2.60 Å R-free 0.236 |
| 6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
1–77（77 aa）
Fragment：UNP residues 1-77
|
Mutation：M77D | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
|
Resolution 2.60 Å R-free 0.236 |
| 6ASR REV1 UBM2 domain complex with ubiquitin Deposited 2017-08-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Fragment：residues 1-76
|
Not recorded | NI NICKEL (II) ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1 M MES pH 6.0, 10 % PEG 8000
|
Resolution 2.36 Å R-free 0.229 |
| 6ASR REV1 UBM2 domain complex with ubiquitin Deposited 2017-08-25 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
Fragment：residues 1-76
|
Not recorded | NI NICKEL (II) ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1 M MES pH 6.0, 10 % PEG 8000
|
Resolution 2.36 Å R-free 0.229 |
| 6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
76–152（77 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000
|
Resolution 2.66 Å R-free 0.263 |
| 6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
76–152（77 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000
|
Resolution 2.66 Å R-free 0.263 |
| 6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
76–152（77 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
|
Resolution 2.61 Å R-free 0.294 |
| 6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain H
76–152（77 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
|
Resolution 2.61 Å R-free 0.294 |
| 6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
76–152（77 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
|
Resolution 2.61 Å R-free 0.294 |
| 6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain H
77–152（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350
|
Resolution 3.27 Å R-free 0.317 |
| 6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
77–152（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350
|
Resolution 3.27 Å R-free 0.317 |
| 6CP2 SidC in complex with UbcH7~Ub Deposited 2018-03-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
75–152（78 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；16% PEG 3000, 0.1 M Tris pH 9.0
|
Resolution 2.90 Å R-free 0.288 |
| 6DGF Ubiquitin Variant bound to USP2 Deposited 2018-05-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
153–226（74 aa）
|
Mutation：Q2C, K6C, K11R, T12C | ZN ZINC ION × 1 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M MES buffer pH 6, 12% (w/v) PEG3350, 0.2M sodium sulfate
|
Resolution 2.34 Å R-free 0.224 |
| 6EI1 Crystal structure of the covalent complex between deubiquitinase ZUFSP (ZUP1) and Ubiquitin-PA Deposited 2017-09-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 GOL GLYCEROL × 1 MLI MALONATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5；277 K；0.2 M sodium malonate pH 5, 20 % PEG 3350
|
Resolution 1.73 Å R-free 0.203 |
| 6FDK Structure of Chlamydia trachomatis effector protein Cdu1 bound to ubiquitin Deposited 2017-12-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Not recorded | CL CHLORIDE ION × 1 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M MES pH 6.5, 12% PEG 20000
|
Resolution 1.60 Å R-free 0.203 |
| 6FGE Crystal structure of human ZUFSP/ZUP1 in complex with ubiquitin Deposited 2018-01-10 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MLI MALONATE ION × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 2 FMT FORMIC ACID × 7 PEG DI(HYDROXYETHYL)ETHER × 1 NH4 AMMONIUM ION × 2 ACT ACETATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；4% v/v Tacsimate pH 5.0 and 12% w/v Polyethylene glycol 3,350.
|
Resolution 1.74 Å R-free 0.209 |
| 6FTX Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome Deposited 2018-02-25 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain N
1–76（76 aa）
Chain O
1–76（76 aa）
|
Not recorded | BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 6FX4 Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C Deposited 2018-03-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Mutation：G76C | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.36M tri-Sodium citrat pH6.5, 15% (v/v) Glycerol
|
Resolution 2.50 Å R-free 0.239 |
| 6FX4 Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C Deposited 2018-03-08 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Mutation：G76C | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.36M tri-Sodium citrat pH6.5, 15% (v/v) Glycerol
|
Resolution 2.50 Å R-free 0.239 |
| 6FYH Disulfide between ubiquitin G76C and the E3 HECT ligase Huwe1 Deposited 2018-03-12 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Mutation：G76C | SO4 SULFATE ION × 2 ZN ZINC ION × 6 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.8M Zn SO4 0.1M Na Acetat pH 4.0
|
Resolution 2.91 Å R-free 0.266 |
| 6GLC Structure of phospho-Parkin bound to phospho-ubiquitin Deposited 2018-05-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 6 GOL GLYCEROL × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.03 M of each sodium nitrate, disodium hydrogen phosphate, ammonium sulphate, 0.1 M MOPS/HEPES-Na (pH 7.5)
|
Resolution 1.80 Å R-free 0.205 |
| 6GZS Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to ubiquitin Deposited 2018-07-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Not recorded | GOL GLYCEROL × 1 SO4 SULFATE ION × 1 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MES (pH 6.0), 20% PEG 6000
|
Resolution 1.90 Å R-free 0.213 |
| 6H4H Usp28 catalytic domain variant E593D in complex with UbPA Deposited 2018-07-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
1–75（75 aa）
Chain D
1–75（75 aa）
|
Not recorded | SO4 SULFATE ION × 1 AYE prop-2-en-1-amine × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；273 K；0.1 M Citrate pH 5.0
0.8 M Ammonium Sulfate
|
Resolution 3.50 Å R-free 0.280 |
| 6HEI Structure of the catalytic domain of USP28 (insertion deleted) bound to Ubiquitin-PA Deposited 2018-08-20 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
77–151（75 aa）
|
Mutation：residue 76 replaced with PA warhead Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；22% (w/v) PEG 3350, 300 mM potassium sodium tartrate
|
Resolution 1.64 Å R-free 0.214 |
| 6HEK Structure of human USP28 bound to Ubiquitin-PA Deposited 2018-08-20 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
77–152（76 aa）
Chain D
77–152（76 aa）
|
Mutation：residue 76 replaced with PA warhead Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：residue 76 replaced with PA warhead Non-standard monomer：Yes (specific site not provided by mmCIF) | PG4 TETRAETHYLENE GLYCOL × 2 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.4；291 K；8% (w/v) PEG 3350, 200 mM ammonium acetate and 100 mM sodium citrate pH 5.4
|
Resolution 3.03 Å R-free 0.237 |
| 6HPR Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub Deposited 2018-09-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
75–152（78 aa）
Chain D
75–152（78 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M ammonium fluoride and 15% (w/v) PEG 3350
|
Resolution 1.70 Å R-free 0.197 |
| 6IF1 Crystal structure of Ube2K and K48-linked di-ubiquitin complex Deposited 2018-09-18 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；Tris-HCl,
polyethylene glycol 3350,
ammonium acetate.
|
Resolution 2.47 Å R-free 0.236 |
| 6IF1 Crystal structure of Ube2K and K48-linked di-ubiquitin complex Deposited 2018-09-18 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；Tris-HCl,
polyethylene glycol 3350,
ammonium acetate.
|
Resolution 2.47 Å R-free 0.236 |
| 6ISU Crystal structure of Lys27-linked di-ubiquitin in complex with its selective interacting protein UCHL3 Deposited 2018-11-19 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；18% PEG 3350 (w/v), 400 mM Ca(AC)2
|
Resolution 1.87 Å R-free 0.264 |
| 6JB6 Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.7 A resolution Deposited 2019-01-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, PEG 400, magnesium chloride
|
Resolution 2.70 Å R-free 0.284 |
| 6JB7 Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.1 A resolution Deposited 2019-01-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, PEG 400, magnesium chloride
|
Resolution 2.10 Å R-free 0.250 |
| 6JMA cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Deposited 2019-03-07 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain Y
1–76（76 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.80 Å |
| 6K9P Structure of Deubiquitinase Deposited 2019-06-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
EVAPORATION；291 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350
|
Resolution 2.05 Å R-free 0.210 |
| 6LP2 Structure of Lpg2148/UBE2N-Ub complex Deposited 2020-01-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, potassium citrate
|
Resolution 2.48 Å R-free 0.233 |
| 6MSB Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric（48） Consistent with protein count |
Chain u
1–76（76 aa）
Chain w
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 6MSD Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric（48） Consistent with protein count |
Chain u
1–76（76 aa）
Chain w
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 6MSE Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric（48） Consistent with protein count |
Chain u
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 6MSG Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric（48） Consistent with protein count |
Chain u
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 6N13 UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin Deposited 2018-11-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain D
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 8 | SOLUTION NMR |
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition
0.11 mM [U-13C; U-15N; U-2H] UbcH7, 0.11 mM [U-13C; U-15N; U-2H] ubiquitin, 0.11 mM [U-2H] Parkin -residues 144-465 comprising the RING0-RING1-IBR and RING2(Rcat) domains, 0.11 mM [U-2H] phosphorylated ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 6NJ9 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Deposited 2019-01-02 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain L
1–76（76 aa）
Chain N
1–76（76 aa）
|
Mutation：G76C Mutation：G76C | SAM S-ADENOSYLMETHIONINE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions
Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
|
Resolution 2.96 Å |
| 6OQ1 Crystal Structure of Branched K11/K48-Linked Tri-Ubiquitin Deposited 2019-04-25 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–76（76 aa）
Chain C
1–76（76 aa）
Chain F
1–77（77 aa）
|
Mutation：K11R, K48C, K63R Mutation：K48R Mutation：M77D | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；bis-tris, sodium chloride, PEG 3350
|
Resolution 2.20 Å R-free 0.230 |
| 6OQ1 Crystal Structure of Branched K11/K48-Linked Tri-Ubiquitin Deposited 2019-04-25 | Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
Chain D
1–76（76 aa）
Chain E
1–77（77 aa）
|
Mutation：K11R, K48C, K63R Mutation：K48R Mutation：M77D | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；bis-tris, sodium chloride, PEG 3350
|
Resolution 2.20 Å R-free 0.230 |
| 6OQ2 NMR Structure of Branched K11/K48-Linked Tri-Ubiquitin Deposited 2019-04-25 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
Chain D
1–76（76 aa）
Chain E
1–77（77 aa）
|
Mutation：K11R, K48R, K63R Mutation：K48R Mutation：M77D | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.8；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition
120 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
100 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
60 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
110 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 6PGV Human Josephin-2 in complex with ubiquitin Deposited 2019-06-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Not recorded | NEH ETHANAMINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
MICROBATCH；pH 4.6；293 K；0.1 M sodium acetate pH 4.6, 0.2 M CaCl2, 22.5% (w/v) PEG 6000; microbatch under Al's Oil
|
Resolution 2.30 Å R-free 0.224 |
| 6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
77–150（74 aa）
Chain B
77–150（74 aa）
|
Mutation：G10V Mutation：G10V | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride
dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
|
Resolution 2.23 Å R-free 0.281 |
| 6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
77–150（74 aa）
Chain D
77–150（74 aa）
|
Mutation：G10V Mutation：G10V | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride
dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
|
Resolution 2.23 Å R-free 0.281 |
| 6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
77–150（74 aa）
Chain F
77–150（74 aa）
|
Mutation：G10V Mutation：G10V | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride
dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
|
Resolution 2.23 Å R-free 0.281 |
| 6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 | Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
77–150（74 aa）
Chain H
77–150（74 aa）
|
Mutation：G10V Mutation：G10V | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride
dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
|
Resolution 2.23 Å R-free 0.281 |
| 6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 | Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain I
77–150（74 aa）
Chain J
77–150（74 aa）
|
Mutation：G10V Mutation：G10V | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride
dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
|
Resolution 2.23 Å R-free 0.281 |
| 6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 | Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain K
77–150（74 aa）
Chain L
77–150（74 aa）
|
Mutation：G10V Mutation：G10V | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride
dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
|
Resolution 2.23 Å R-free 0.281 |
| 6QML UCHL3 in complex with synthetic, K27-linked diubiquitin Deposited 2019-02-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–76（76 aa）
|
Mutation：M1(NLE) Non-standard monomer：Yes (specific site not provided by mmCIF) | K POTASSIUM ION × 2 BR BROMIDE ION × 3 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops.
Best crystals:
21% PEG 3350
0.15M KBr
0.1M Bis-Tris pH 5.5
Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.
|
Resolution 2.10 Å R-free 0.233 |
| 6QML UCHL3 in complex with synthetic, K27-linked diubiquitin Deposited 2019-02-07 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain E
1–76（76 aa）
|
Mutation：M1(NLE) Non-standard monomer：Yes (specific site not provided by mmCIF) | K POTASSIUM ION × 3 BR BROMIDE ION × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops.
Best crystals:
21% PEG 3350
0.15M KBr
0.1M Bis-Tris pH 5.5
Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.
|
Resolution 2.10 Å R-free 0.233 |
| 6UD0 Solution-state NMR structural ensemble of human Tsg101 UEV in complex with K63-linked diubiquitin Deposited 2019-09-18 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–76（76 aa）
Chain B
1–77（77 aa）
|
Mutation：K63R Mutation：+D77 | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 5.8；300 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1
NMR sample composition
200 uM [U-98% 15N] Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
200 uM Tsg101 UEV domain, 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
200 uM Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
200 uM [U-98% 15N] Tsg101 UEV domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 6UYI hRpn13:hRpn2:K48-diubiquitin Deposited 2019-11-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
1–77（77 aa）
Chain D
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.5；298.15 K；Ionic strength (raw mmCIF value) 0.11；Pressure ambient
NMR sample composition
0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2O | 100% D2O
NMR sample composition
0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM proximal ubiquitin, 0.72 mM [U-13C] distal ubiquitin, 100% D2O | 100% D2O
|
Resolution not provided |
| 6UYJ hRpn13:hRpn2:K48-diubiquitin Deposited 2019-11-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
1–77（77 aa）
Chain D
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.5；298.15 K；Ionic strength (raw mmCIF value) 0.11；Pressure ambient
NMR sample composition
0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2O | 100% D2O
NMR sample composition
0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2O | 100% D2O
|
Resolution not provided |
| 6XZ1 Conjugate of the HECT domain of HUWE1 with ubiquitin Deposited 2020-01-31 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–75（75 aa）
|
Not recorded | PO4 PHOSPHATE ION × 2 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.65 M Sodium phosphate monobasic, potassium phosphate dibasic, 0.1 M HEPES pH 7.5
|
Resolution 2.30 Å R-free 0.255 |
| 6XZ1 Conjugate of the HECT domain of HUWE1 with ubiquitin Deposited 2020-01-31 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–75（75 aa）
|
Not recorded | PO4 PHOSPHATE ION × 3 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.65 M Sodium phosphate monobasic, potassium phosphate dibasic, 0.1 M HEPES pH 7.5
|
Resolution 2.30 Å R-free 0.255 |
| 7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain CCC
75–152（78 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
|
Resolution 1.82 Å R-free 0.231 |
| 7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain FFF
75–152（78 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
|
Resolution 1.82 Å R-free 0.231 |
| 7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 | Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain III
75–152（78 aa）
|
Not recorded | ZN ZINC ION × 2 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
|
Resolution 1.82 Å R-free 0.231 |
| 7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 | Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain LLL
75–152（78 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
|
Resolution 1.82 Å R-free 0.231 |
| 7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain CCC
75–152（78 aa）
|
Not recorded | CL CHLORIDE ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
|
Resolution 1.56 Å R-free 0.185 |
| 7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain FFF
75–152（78 aa）
|
Not recorded | CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
|
Resolution 1.56 Å R-free 0.185 |
| 7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain CCC
75–152（78 aa）
|
Not recorded | CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
|
Resolution 2.07 Å R-free 0.266 |
| 7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain FFF
75–152（78 aa）
|
Not recorded | CL CHLORIDE ION × 1 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
|
Resolution 2.07 Å R-free 0.266 |
| 7AY2 Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg Deposited 2020-11-10 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；292 K；8-13% w/v PEG3350, 0.1 M citric acid/Bis-Tris propane pH 4.1
|
Resolution 3.20 Å R-free 0.234 |
| 7AY2 Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg Deposited 2020-11-10 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain F
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；292 K；8-13% w/v PEG3350, 0.1 M citric acid/Bis-Tris propane pH 4.1
|
Resolution 3.20 Å R-free 0.234 |
| 7CAP Cyclic Lys48-linked triubiquitin Deposited 2020-06-09 | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 6 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；20% PEG 3350, 200 mM zinc acetate
|
Resolution 1.33 Å R-free 0.174 |
| 7DNI MDA5 CARDs-MAVS CARD polyUb complex Deposited 2020-12-09 | Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein count |
Chain E
1–76（76 aa）
Chain F
1–76（76 aa）
Chain G
1–76（76 aa）
Chain H
1–76（76 aa）
Chain I
1–76（76 aa）
Chain J
1–76（76 aa）
Chain K
1–76（76 aa）
Chain L
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
|
Resolution 3.20 Å |
| 7DNJ K63-polyUb MDA5CARDs complex Deposited 2020-12-09 | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count |
Chain E
1–76（76 aa）
Chain F
1–76（76 aa）
Chain G
1–76（76 aa）
Chain H
1–76（76 aa）
Chain I
1–76（76 aa）
Chain J
1–76（76 aa）
Chain K
1–76（76 aa）
Chain L
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 3.30 Å |
| 7F7X Protein complex between phosphorylated ubiquitin and Ubqln2 UBA Deposited 2021-06-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition
20 mM HEPES, 0.15 M sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Not recorded | CA CALCIUM ION × 3 AYE prop-2-en-1-amine × 1 GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
|
Resolution 2.78 Å R-free 0.273 |
| 7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–75（75 aa）
|
Not recorded | CA CALCIUM ION × 3 AYE prop-2-en-1-amine × 1 GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
|
Resolution 2.78 Å R-free 0.273 |
| 7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–75（75 aa）
|
Not recorded | CA CALCIUM ION × 2 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
|
Resolution 2.78 Å R-free 0.273 |
| 7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
1–75（75 aa）
|
Not recorded | CA CALCIUM ION × 1 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
|
Resolution 2.78 Å R-free 0.273 |
| 7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain K
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Not recorded | GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0
29% PEG3350
40 mM DL-Malic acid
5 mM DTT
|
Resolution 2.47 Å R-free 0.276 |
| 7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Not recorded | GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0
29% PEG3350
40 mM DL-Malic acid
5 mM DTT
|
Resolution 2.47 Å R-free 0.276 |
| 7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–76（76 aa）
|
Not recorded | GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0
29% PEG3350
40 mM DL-Malic acid
5 mM DTT
|
Resolution 2.47 Å R-free 0.276 |
| 7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
1–76（76 aa）
|
Not recorded | GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0
29% PEG3350
40 mM DL-Malic acid
5 mM DTT
|
Resolution 2.47 Å R-free 0.276 |
| 7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 3 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
|
Resolution 3.10 Å R-free 0.257 |
| 7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
|
Resolution 3.10 Å R-free 0.257 |
| 7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 3 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
|
Resolution 3.10 Å R-free 0.257 |
| 7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
|
Resolution 3.10 Å R-free 0.257 |
| 7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain J
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
|
Resolution 3.10 Å R-free 0.257 |
| 7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain L
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
|
Resolution 3.10 Å R-free 0.257 |
| 7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain N
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
|
Resolution 3.10 Å R-free 0.257 |
| 7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain P
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
|
Resolution 3.10 Å R-free 0.257 |
| 7MEY Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron Deposited 2021-04-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain C
1–75（75 aa）
Fragment：K48C
Chain D
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 7 Z3V 2-(ethylamino)ethane-1-thiol × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.67 Å |
| 7MYF Ubiquitin variant UbV.k.1 in complex with Ube2k Deposited 2021-05-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Mutation：Q31F, G21R, T23Y, A57S, K59Q, K74E, E75F, T77F, V81I, L82S | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2-0.3 M ammonium citrate dibasic, 20-25% PEG3350
|
Resolution 3.00 Å R-free 0.293 |
| 7MYH Ubiquitin variant UbV.k.2 in complex with Ube2k Deposited 2021-05-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Mutation：K6S, L8F, T9V, K11L, T14M, K63N, E64D, T66I, H68R, L71I, G76L | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M sodium citrate tribasic trihydrate, 0.1 M Bis-Tris propane, pH 7.5, 20% PEG3350
|
Resolution 2.39 Å R-free 0.249 |
| 7OJE Crystal structure of the covalent complex between Tribolium castaneum deubiquitinase ZUP and Ubiquitin-PA Deposited 2021-05-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1 NA SODIUM ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；8 % (v/v) Tacsimate pH 7; 22 %PEG3350
|
Resolution 2.05 Å R-free 0.219 |
| 7OJE Crystal structure of the covalent complex between Tribolium castaneum deubiquitinase ZUP and Ubiquitin-PA Deposited 2021-05-14 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；8 % (v/v) Tacsimate pH 7; 22 %PEG3350
|
Resolution 2.05 Å R-free 0.219 |
| 7OJX E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for K48-linked Ub chain synthesis Deposited 2021-05-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
Chain E
1–76（76 aa）
|
Mutation：K48C | ZN ZINC ION × 2 ME7 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione) × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；Crystals were grown in: 0.2 M sodium citrate, 0.1 M Bis Tris propane 7.5 and 20 % (w/v) PEG 3350. The crystallization drops were set as a 1:1 mixture of the protein complex solution and the precipitant solution.
|
Resolution 2.40 Å R-free 0.236 |
| 7QO5 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state Deposited 2021-12-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric（49） Consistent with protein count |
Chain 9
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.00 Å |
| 7RBR The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with a Lys48-linked di-ubiquitin Deposited 2021-07-06 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–77（77 aa）
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.2 M di-sodium tartrate, 20% PEG-3350,
|
Resolution 1.88 Å R-free 0.228 |
| 7RMA Structure of the fourth UIM (Ubiquitin Interacting Motif) of ANKRD13D in complex with a high affinity UbV (Ubiquitin Variant) Deposited 2021-07-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
1–79（79 aa）
|
Not recorded | SO4 SULFATE ION × 2 NA SODIUM ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1M Li2SO4, 0.1M sodium acetate pH 4.5 and 50% PEG 400. Crystals were cryoprotected in this buffer plus 20% ethylene glycol
|
Resolution 2.00 Å R-free 0.246 |
| 7S6O The crystal structure of Lys48-linked di-ubiquitin Deposited 2021-09-14 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
|
Mutation：K48R Mutation：Aspartic acid residue added to C terminus (D77) | ACT ACETATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.8；289 K；50 mM acetate, 8.6% PEG2000 MME, 17.1% PEG400
|
Resolution 1.25 Å R-free 0.175 |
| 7UV5 The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a Lys48-linked di-ubiquitin Deposited 2022-04-29 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–76（76 aa）
|
Mutation：K48R | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.2 M sodium tartrate, 15% PEG3350
|
Resolution 1.45 Å R-free 0.179 |
| 7W38 Structure of USP14-bound human 26S proteasome in state EA2.0_UBL Deposited 2021-11-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric（48） Consistent with protein count |
Chain u
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7W39 Structure of USP14-bound human 26S proteasome in state EA2.1_UBL Deposited 2021-11-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric（49） Consistent with protein count |
Chain u
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7W3A Structure of USP14-bound human 26S proteasome in substrate-engaged state ED4_USP14 Deposited 2021-11-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric（49） Consistent with protein count |
Chain y
1–76（76 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7W3B Structure of USP14-bound human 26S proteasome in substrate-engaged state ED5_USP14 Deposited 2021-11-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric（49） Consistent with protein count |
Chain y
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7W3C Structure of USP14-bound human 26S proteasome in substrate-engaged state ED0_USP14 Deposited 2021-11-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric（49） Consistent with protein count |
Chain y
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7W3F Structure of USP14-bound human 26S proteasome in substrate-engaged state ED1_USP14 Deposited 2021-11-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric（49） Consistent with protein count |
Chain y
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7W3G Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.0_USP14 Deposited 2021-11-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric（49） Consistent with protein count |
Chain y
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7W3H Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.1_USP14 Deposited 2021-11-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric（49） Consistent with protein count |
Chain y
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7W3I Structure of USP14-bound human 26S proteasome in substrate-inhibited state SB_USP14 Deposited 2021-11-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric（48） Consistent with protein count |
Chain y
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7W3J Structure of USP14-bound human 26S proteasome in substrate-inhibited state SC_USP14 Deposited 2021-11-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric（48） Consistent with protein count |
Chain y
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.50 Å |
| 7W3K Structure of USP14-bound human 26S proteasome in substrate-inhibited state SD4_USP14 Deposited 2021-11-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric（48） Consistent with protein count |
Chain y
1–76（76 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7W3M Structure of USP14-bound human 26S proteasome in substrate-inhibited state SD5_USP14 Deposited 2021-11-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric（48） Consistent with protein count |
Chain y
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7XCR Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex Deposited 2022-03-25 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain L
1–76（76 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.57 Å |
| 7XCT Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex Deposited 2022-03-25 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain L
1–76（76 aa）
Chain N
1–76（76 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.72 Å |
| 8BS9 Structure of USP36 in complex with Ubiquitin-PA Deposited 2022-11-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.3 M potassium formate, 14% (w/v) PEG 3350
|
Resolution 1.90 Å R-free 0.209 |
| 8BS9 Structure of USP36 in complex with Ubiquitin-PA Deposited 2022-11-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.3 M potassium formate, 14% (w/v) PEG 3350
|
Resolution 1.90 Å R-free 0.209 |
| 8C07 Structure of HECT E3 UBR5 forming K48 linked Ubiquitin chains Deposited 2022-12-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain I
1–76（76 aa）
Chain K
1–76（76 aa）
|
Not recorded | SY8 5-azanylpentan-2-one × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8C61 Structure of USP54 in complex with Lys63-linked diUbiquitin-PA Deposited 2023-01-11 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain B
1–75（75 aa）
Chain C
1–76（76 aa）
Chain E
1–75（75 aa）
Chain F
1–76（76 aa）
|
Mutation：K63R Mutation：K63R | ZN ZINC ION × 6 AYE prop-2-en-1-amine × 2 CL CHLORIDE ION × 2 NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；27.2 % (v/v) PEG 400, 0.1 M HEPES, 0.2 M calcium chloride
|
Resolution 2.50 Å R-free 0.243 |
| 8C61 Structure of USP54 in complex with Lys63-linked diUbiquitin-PA Deposited 2023-01-11 | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain H
1–75（75 aa）
Chain I
1–76（76 aa）
Chain K
1–75（75 aa）
Chain L
1–76（76 aa）
|
Mutation：K63R Mutation：K63R | ZN ZINC ION × 6 AYE prop-2-en-1-amine × 2 NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；27.2 % (v/v) PEG 400, 0.1 M HEPES, 0.2 M calcium chloride
|
Resolution 2.50 Å R-free 0.243 |
| 8DMQ Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester Deposited 2022-07-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–75（75 aa）
|
Not recorded | FLC CITRATE ANION × 4 EDO 1,2-ETHANEDIOL × 2 GVE METHYL 4-AMINOBUTANOATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
|
Resolution 2.19 Å R-free 0.209 |
| 8DMQ Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester Deposited 2022-07-08 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–75（75 aa）
|
Not recorded | FLC CITRATE ANION × 1 EDO 1,2-ETHANEDIOL × 1 GVE METHYL 4-AMINOBUTANOATE × 1 1PE PENTAETHYLENE GLYCOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
|
Resolution 2.19 Å R-free 0.209 |
| 8DMS Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose Deposited 2022-07-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–75（75 aa）
|
Not recorded | 1PE PENTAETHYLENE GLYCOL × 1 GVE METHYL 4-AMINOBUTANOATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
|
Resolution 2.15 Å R-free 0.207 |
| 8DMS Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose Deposited 2022-07-08 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–75（75 aa）
|
Not recorded | AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 GVE METHYL 4-AMINOBUTANOATE × 1 FLC CITRATE ANION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
|
Resolution 2.15 Å R-free 0.207 |
| 8EFW Structure of SdeA DUB Domain disulfide crosslinked with Ubiquitin Deposited 2022-09-09 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；2.8M sodium acetate: HCl pH7
|
Resolution 2.81 Å |
| 8EFX Structure of OtDUB DUB Domain disulfide crosslinked with Ubiquitin Deposited 2022-09-09 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；294 K；0.16M Magnesium chloride, 0.08M Tris at pH 8.5, 24% PEG 8000 and 20% glycerol
|
Resolution 1.85 Å R-free 0.229 |
| 8EHO PRRSV-1 PLP2 domain bound to ubiquitin Deposited 2022-09-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 GOL GLYCEROL × 2 3CN 3-AMINOPROPANE × 1 NO3 NITRATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2M Mg(NO3)2
|
Resolution 2.85 Å R-free 0.247 |
| 8EHO PRRSV-1 PLP2 domain bound to ubiquitin Deposited 2022-09-14 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 GOL GLYCEROL × 3 3CN 3-AMINOPROPANE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2M Mg(NO3)2
|
Resolution 2.85 Å R-free 0.247 |
| 8EHO PRRSV-1 PLP2 domain bound to ubiquitin Deposited 2022-09-14 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–75（75 aa）
|
Not recorded | ZN ZINC ION × 1 GOL GLYCEROL × 2 3CN 3-AMINOPROPANE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2M Mg(NO3)2
|
Resolution 2.85 Å R-free 0.247 |
| 8F1F Structure of K48-linked tri-ubiquitin in complex with cyclic peptide Deposited 2022-11-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
|
Mutation：D77 added to the C-terminus Mutation：K48R | GOL GLYCEROL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Droplets were formed by mixing equal volumes of Ub3:Ub4a complex (8 mg/ml) and the crystallization solution containing 0.15 M NaCl, 23% (w/v) PEG 3350 and 0.1 M HEPES (pH 7.5)
|
Resolution 1.85 Å R-free 0.298 |
| 8F1F Structure of K48-linked tri-ubiquitin in complex with cyclic peptide Deposited 2022-11-05 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain a
1–76（76 aa）
Chain b
1–76（76 aa）
Chain c
1–76（76 aa）
|
Mutation：D77 added to the C-terminus Mutation：K48R | EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Droplets were formed by mixing equal volumes of Ub3:Ub4a complex (8 mg/ml) and the crystallization solution containing 0.15 M NaCl, 23% (w/v) PEG 3350 and 0.1 M HEPES (pH 7.5)
|
Resolution 1.85 Å R-free 0.298 |
| 8G6G H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5 Deposited 2023-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain K
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.93 Å |
| 8G6H H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6 Deposited 2023-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain K
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.06 Å |
| 8G6Q H2AK119ub-modified nucleosome ubiquitin position 1 Deposited 2023-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain K
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.41 Å |
| 8G6S H2AK119ub-modified nucleosome ubiquitin position 2 Deposited 2023-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain K
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 8GRM Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Deposited 2022-09-02 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain O
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å |
| 8H1T Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Deposited 2022-10-04 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain M
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8IC9 Lys48-linked K48C-diubiquitin Deposited 2023-02-11 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
|
Mutation：K48C | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；38% 2-methyl-2,4-pentanediol and 50 mM sodium citrate (pH 4.0)
|
Resolution 1.25 Å R-free 0.219 |
| 8IC9 Lys48-linked K48C-diubiquitin Deposited 2023-02-11 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
|
Mutation：K48C | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；38% 2-methyl-2,4-pentanediol and 50 mM sodium citrate (pH 4.0)
|
Resolution 1.25 Å R-free 0.219 |
| 8ITP Crystal structure of USP47 catalytic domain complex with ubiquitin Deposited 2023-03-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM bis-Tris (pH 5.5),
25% PEG 3350,
50 mM MgCl2
|
Resolution 3.00 Å R-free 0.284 |
| 8ITP Crystal structure of USP47 catalytic domain complex with ubiquitin Deposited 2023-03-22 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
1–76（76 aa）
|
Not recorded | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM bis-Tris (pH 5.5),
25% PEG 3350,
50 mM MgCl2
|
Resolution 3.00 Å R-free 0.284 |
| 8J1P Cryo-EM structure of Ufd4 in complex with K29/48 triUb Deposited 2023-04-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
1–76（76 aa）
Chain D
1–76（76 aa）
Chain E
1–76（76 aa）
|
Mutation：K29C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.31 Å |
| 8JRT Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) bound to K11/K48-branched ubiquitin (Ub) chain composed of three Ub. Deposited 2023-06-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric（28） Consistent with protein count |
Chain u
77–152（76 aa）
Chain v
77–152（76 aa）
Chain w
77–152（76 aa）
|
Mutation：K63R Mutation：K63R Mutation：K63R | ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；incubation time= 3 s
blotting time= 2.5 s
|
Resolution 3.60 Å |
| 8JTI Cryo-EM structure of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub. Deposited 2023-06-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 29 PDB declaration: 29-meric（29） Consistent with protein count |
Chain u
77–152（76 aa）
Chain v
77–152（76 aa）
Chain w
77–152（76 aa）
Chain x
77–152（76 aa）
|
Mutation：K63R Mutation：K63R Mutation：K63R Mutation：K63R | ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；incubation time= 3 s
blotting time= 2.5 s
|
Resolution 3.80 Å |
| 8K0G Cryo-EM structure of human 26S RP (Ed state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub. Deposited 2023-07-09 | Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric（30） Consistent with protein count |
Chain u
77–152（76 aa）
Chain v
77–152（76 aa）
Chain w
77–152（76 aa）
Chain x
77–152（76 aa）
|
Mutation：K63R Mutation：K63R Mutation：K63R Mutation：K63R | ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；incubation time= 3 s
blotting time= 2.5 s
|
Resolution 3.80 Å |
| 8K6F LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain E
1–76（76 aa）
Chain F
1–76（76 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 2 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
EVAPORATION；289 K；PEG8000, Sodium Choride, Sodium HEPES
|
Resolution 3.41 Å R-free 0.243 |
| 8K6R LnaB-Actin-PRUb ternary complex in the presence of AMPPNP Deposited 2023-07-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
EVAPORATION；289 K；Sodium Chloride, Sodium HEPES, PEG8000
|
Resolution 2.76 Å R-free 0.261 |
| 8K6V LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
EVAPORATION；289 K；Magnesium acetate, MOPS, PEG8000
|
Resolution 2.60 Å R-free 0.307 |
| 8OYP Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic Deposited 2023-05-05 | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | CD CADMIUM ION × 1 CL CHLORIDE ION × 1 NO3 NITRATE ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；100 mM Tris/Bicine pH 8.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 11.25% v/v MPD; 11.25% PEG 1000; 11.25% w/v PEG 3350 with 5 mM CdCl2
|
Resolution 2.44 Å R-free 0.235 |
| 8OYP Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic Deposited 2023-05-05 | Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Not recorded | CD CADMIUM ION × 1 CL CHLORIDE ION × 1 NO3 NITRATE ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；100 mM Tris/Bicine pH 8.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 11.25% v/v MPD; 11.25% PEG 1000; 11.25% w/v PEG 3350 with 5 mM CdCl2
|
Resolution 2.44 Å R-free 0.235 |
| 8Q00 TssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430) reacted with Ub-PA Deposited 2023-07-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium citrate dibasic and 22 % w/v PEG 3350; 1:2, 1:1, 2:1 protein:reservoir ration; cryoprotected with reservoir + 25% ethylene glycol
|
Resolution 1.62 Å R-free 0.198 |
| 8Q00 TssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430) reacted with Ub-PA Deposited 2023-07-27 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium citrate dibasic and 22 % w/v PEG 3350; 1:2, 1:1, 2:1 protein:reservoir ration; cryoprotected with reservoir + 25% ethylene glycol
|
Resolution 1.62 Å R-free 0.198 |
| 8RQI Structure of Rhizobium NopD with ubiquitin Deposited 2024-01-18 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M imidazole 8.0 and 10% PEG8000
|
Resolution 1.94 Å R-free 0.199 |
| 8RX0 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub Deposited 2024-02-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count |
Chain U
1–76（76 aa）
|
Not recorded | 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain M
18–76（59 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain M
18–76（59 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain M
18–76（59 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain M
18–76（59 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain M
18–76（59 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain M
18–76（59 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain M
18–76（59 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain M
18–76（59 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain M
18–76（59 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain M
18–76（59 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain M
18–76（59 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8V25 H2BK120ub-modified nucleosome ubiquitin position 1 Deposited 2023-11-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain K
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 8V26 H2BK120ub-modified nucleosome ubiquitin position 2 Deposited 2023-11-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain K
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 8V27 H2BK120ub-modified nucleosome ubiquitin position 3 Deposited 2023-11-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain K
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 8V28 H2BK120ub-modified nucleosome ubiquitin position 4 Deposited 2023-11-22 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain K
1–76（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.36 Å |
| 8W31 Crystal structure of parkin (R0RB):2pUb with activator compound Deposited 2024-02-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–75（75 aa）
Fragment：residues 1-75
Chain C
1–75（75 aa）
Fragment：residues 1-75
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 6 A1AE9 (S)-1-(6-benzyl-3-(4-(1,2,3,4-tetrahydroquinoline-1-carbonyl)phenyl)-6,7-dihydropyrazolo[1,5-a]pyrazin-5(4H)-yl)ethan-1-one × 1 GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M Sodium Chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350
|
Resolution 2.50 Å R-free 0.294 |
| 8XEP Crystal structure of a Legionella pneumophila type IV effector in complex with ubiquitin Deposited 2023-12-12 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
1–76（76 aa）
Chain C
1–76（76 aa）
|
Not recorded | SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；100 mM sodium acetate, pH 6.0, 160 mM ammonium sulfate, 21% PEG 4000, 20% glycerol
|
Resolution 2.95 Å R-free 0.228 |
| 9AVT Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin Deposited 2024-03-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–76（76 aa）
Chain B
1–76（76 aa）
|
Not recorded | SO4 SULFATE ION × 4 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2.2 M ammonium sulphate
|
Resolution 1.50 Å R-free 0.203 |
| 9AVW Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin Deposited 2024-03-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
1–152（152 aa）
Chain B
1–152（152 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 6 ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；2.2 M ammonium sulphate, 20% glycerol
|
Resolution 1.75 Å R-free 0.222 |
| 9AZJ Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1 Deposited 2024-03-11 | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric（9） Consistent with protein count |
Chain F
1–76（76 aa）
Chain S
1–76（76 aa）
Chain Z
1–76（76 aa）
|
Mutation：G76C Mutation：G76C Mutation：G76C | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.6；293 K；150nl protein + 50 nl mother liquor: 0.1 M Tris/Bicine pH 8.6, 24.2% PEG 500 MME, 8% PEG 20K, 0.03 M each of NaI, NaBr, and NaF. Cryoprotected in mother liquor containing 20% glycerol
|
Resolution 3.32 Å R-free 0.285 |
| 9B0Z Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 2 Deposited 2024-03-12 | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count |
Chain C
1–152（152 aa）
Chain D
1–152（152 aa）
Chain G
1–152（152 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；293 K；20% PEG 2K MME, 0.2 M TAO and 0.1 M Tris pH 8.5. Cryoprotected in mother liquor containing 20% glycerol
|
Resolution 2.41 Å R-free 0.270 |
| 9B12 Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1 Deposited 2024-03-12 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain B
1–152（152 aa）
|
Not recorded | PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；3:1 with reservoir solution containing 50% PEG 200 and 0.1 M HEPES pH 7.5
|
Resolution 1.81 Å R-free 0.269 |
| 9B12 Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1 Deposited 2024-03-12 | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain A
1–152（152 aa）
|
Not recorded | PG4 TETRAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；3:1 with reservoir solution containing 50% PEG 200 and 0.1 M HEPES pH 7.5
|
Resolution 1.81 Å R-free 0.269 |
| 9C5E Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin Deposited 2024-06-06 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 | SOLUTION NMR |
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition
300 uM [U-13C; U-15N] Rcat domain from Parkin, 300 uM Ubiquitin G75-C3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
800 uM [U-13C; U-15N] Rcat domain from Parkin, 800 uM Ubiquitin G75-C3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
300 uM [U-13C; U-15N] Ubiquitin G75-C3, 300 uM Rcat domain from Parkin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
300 uM [U-13C; U-15N] Rcat domain from Parkin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
500 uM [U-13C; U-15N] Ubiquitin G75-C3, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 9D1I Structure of Ubiquitin bound to KLHDC3-EloB/C Deposited 2024-08-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain D
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；10%PEG5KMME,
0.1M HEPES pH=7.0,
5% Tascsimate pH=7.0
|
Resolution 2.00 Å R-free 0.189 |
| 9DBY ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Deposited 2024-08-24 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain N
1–76（76 aa）
|
Mutation：G76C | ZN ZINC ION × 5 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9DDE ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Deposited 2024-08-28 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric（15） Consistent with all polymers |
Chain N
1–76（76 aa）
|
Mutation：G76C | ZN ZINC ION × 5 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9DG3 ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome Deposited 2024-09-01 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain N
1–76（76 aa）
|
Mutation：G76C | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.46 Å |
| 9EBS Cryo-EM structure of USP1-UAF1-Ubiquitin in complex with TNG348 Deposited 2024-11-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–75（75 aa）
|
Not recorded | A1A4Y 3-(methanesulfonyl)propan-1-amine × 1 ZN ZINC ION × 1 A1BHF 2-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-9-({4-[1-methyl-4-(trifluoromethyl)-1H-imidazol-2-yl]phenyl}methyl)-7-(2,2,2-trifluoroethyl)-7,9-dihydro-8H-purin-8-imine × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9EMK DupA from legionella covalently bound to ubiquitin-based probe Deposited 2024-03-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1H50 [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000
0.1 M HEPES pH7
0.2 M MgCl2
|
Resolution 2.17 Å R-free 0.239 |
| 9EMK DupA from legionella covalently bound to ubiquitin-based probe Deposited 2024-03-08 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1H50 [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000
0.1 M HEPES pH7
0.2 M MgCl2
|
Resolution 2.17 Å R-free 0.239 |
| 9EMK DupA from legionella covalently bound to ubiquitin-based probe Deposited 2024-03-08 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1H50 [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000
0.1 M HEPES pH7
0.2 M MgCl2
|
Resolution 2.17 Å R-free 0.239 |
| 9F5T Ubiquitin C-terminal clippase BpJOS Deposited 2024-04-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–152（152 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1 M CHES pH 9.5; 22 % PEG 8000; 1:2 protein reservoir drop ration; cryoprotected with reservoir + 20% Glycerol
|
Resolution 2.56 Å R-free 0.253 |
| 9F5T Ubiquitin C-terminal clippase BpJOS Deposited 2024-04-30 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–152（152 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1 M CHES pH 9.5; 22 % PEG 8000; 1:2 protein reservoir drop ration; cryoprotected with reservoir + 20% Glycerol
|
Resolution 2.56 Å R-free 0.253 |
| 9F6G Human USP30 chimera bound to Ubiquitin-PA Deposited 2024-05-01 | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.56 M sodium citrate pH 7.0
|
Resolution 1.50 Å R-free 0.211 |
| 9FN4 DUBS Parachlamydia sp. PcJOS Deposited 2024-06-09 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–152（152 aa）
|
Not recorded | TLA L(+)-TARTARIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；Molecular Dimensions Morpheus B7, 298 K.
|
Resolution 2.15 Å R-free 0.201 |
| 9FPA DUBS Parachlamydia sp. PcJOS orthorhombic crystal form Deposited 2024-06-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–152（152 aa）
|
Not recorded | CIT CITRIC ACID × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；Midas G6. 35 % v/v glycerol ethoxylate, 0.2 M lithium citrate
|
Resolution 2.18 Å R-free 0.212 |
| 9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
|
Resolution 1.89 Å R-free 0.231 |
| 9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 | Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain T
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
|
Resolution 1.89 Å R-free 0.231 |
| 9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 | Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain V
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
|
Resolution 1.89 Å R-free 0.231 |
| 9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 | Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain X
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
|
Resolution 1.89 Å R-free 0.231 |
| 9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
|
Resolution 1.89 Å R-free 0.231 |
| 9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
|
Resolution 1.89 Å R-free 0.231 |
| 9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
|
Resolution 1.89 Å R-free 0.231 |
| 9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain J
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
|
Resolution 1.89 Å R-free 0.231 |
| 9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain L
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
|
Resolution 1.89 Å R-free 0.231 |
| 9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain N
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
|
Resolution 1.89 Å R-free 0.231 |
| 9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain P
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
|
Resolution 1.89 Å R-free 0.231 |
| 9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 | Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain R
1–75（75 aa）
|
Not recorded | AYE prop-2-en-1-amine × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
|
Resolution 1.89 Å R-free 0.231 |
| 9GKM Structure of HECT E3 TRIP12 forming K29/K48-branched Ubiquitin chains Deposited 2024-08-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain D
1–76（76 aa）
|
Mutation：K48R | SY8 5-azanylpentan-2-one × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.69 Å |
| 9HNW USP1-UAF1 bound to Lys63-linked diubiquitin Deposited 2024-12-11 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
1–75（75 aa）
Chain D
1–76（76 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K63(DAB) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 9ISZ Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation Deposited 2024-07-19 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain C
153–228（76 aa）
Chain D
153–228（76 aa）
|
Mutation：G76C Mutation：G76C | SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0
|
Resolution 2.60 Å R-free 0.274 |
| 9ISZ Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation Deposited 2024-07-19 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
153–228（76 aa）
|
Mutation：G76C | SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0
|
Resolution 2.60 Å R-free 0.274 |
| 9ISZ Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation Deposited 2024-07-19 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
153–228（76 aa）
|
Mutation：G76C | SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0
|
Resolution 2.60 Å R-free 0.274 |
| 9MC6 Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 2 Deposited 2025-03-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 9MC7 Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 4 Deposited 2025-03-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 9MC9 Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 1 Deposited 2025-03-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.37 Å |
| 9MCB Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 1 Deposited 2025-03-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 9QHI Structure of UBA6-UbDha-BIRC6 trapped ternary complex (cluster 0) Deposited 2025-03-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
1–76（76 aa）
Chain E
1–76（76 aa）
|
Not recorded | IHP INOSITOL HEXAKISPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.27 Å |
| 9QUG Structure of a UBC-Ubiquitin conjugate Deposited 2025-04-10 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
1–76（76 aa）
|
Not recorded | GOL GLYCEROL × 4 P4K polyethylene glycol × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% (w/v) Polyethylene glycol monomethyl ether 2,000
|
Resolution 1.80 Å R-free 0.192 |
| 9V33 Calypso/Asx/NCP-ub complex Deposited 2025-05-21 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric（15） Consistent with all polymers |
Chain M
77–151（75 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 5.90 Å |
| 9V9Q Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers |
Chain O
153–228（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 2.80 Å |
| 9V9R Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers |
Chain O
153–228（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.20 Å |
| 9V9S Cryo-EM structure of the ncPRC1.1 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain K
153–228（76 aa）
Chain O
153–228（76 aa）
|
Mutation：G76C Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.80 Å |
| 9V9T Cryo-EM structure of the ncPRC1.6 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain K
153–228（76 aa）
Chain O
153–228（76 aa）
|
Mutation：G76C Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 2.90 Å |
| 9V9U Cryo-EM structure of the ncPRC1.4 complex containing two RNF2-BMI1 bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric（16） Consistent with all polymers |
Chain O
153–228（76 aa）
Chain P
153–228（76 aa）
|
Mutation：G76C Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.70 Å |
| 9V9V Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers |
Chain K
153–228（76 aa）
Chain O
153–228（76 aa）
|
Mutation：G76C Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.80 Å |
| 9V9W Cryo-EM structure of the ncPRC1.4 complex containing two RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain K
153–228（76 aa）
Chain O
153–228（76 aa）
|
Mutation：G76C Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.00 Å |
| 9V9Y Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain K
153–228（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.20 Å |
| 9V9Z Cryo-EM structure of the ncPRC1.4 complex containing one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain O
153–228（76 aa）
|
Mutation：G76C | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.00 Å |
| 9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 | Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric（17） Consistent with all polymers |
Chain O
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.50 Å |
| 9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 | Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric（17） Consistent with all polymers |
Chain O
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.63 Å |
| 9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 | Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers |
Chain O
1–76（76 aa）
Chain U
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.43 Å |
| 9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 | Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers |
Chain O
1–76（76 aa）
Chain U
1–76（76 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.45 Å |