+Open data
-Basic information
Entry | Database: PDB / ID: 1nb8 | ||||||
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Title | Structure of the catalytic domain of USP7 (HAUSP) | ||||||
Components | Ubiquitin carboxyl-terminal hydrolase 7 | ||||||
Keywords | HYDROLASE / UBP / deubiquitination / HAUSP / p53 binding | ||||||
Function / homology | Function and homology information regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity ...regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / negative regulation of TORC1 signaling / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / regulation of protein stability / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / PML body / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Degradation / rhythmic process / p53 binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / protein stabilization / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2.3 Å | ||||||
Authors | Hu, M. / Li, P. / Li, M. / Li, W. / Yao, T. / Wu, J.-W. / Gu, W. / Cohen, R.E. / Shi, Y. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde Authors: Hu, M. / Li, P. / Li, M. / Li, W. / Yao, T. / Wu, J.-W. / Gu, W. / Cohen, R.E. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nb8.cif.gz | 147.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nb8.ent.gz | 122 KB | Display | PDB format |
PDBx/mmJSON format | 1nb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/1nb8 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/1nb8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41426.395 Da / Num. of mol.: 2 / Fragment: HAUSP core domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP7 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, EC: 3.1.2.15 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.19 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 1000, Tris, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 30, 2002 |
Radiation | Monochromator: yale mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→99 Å / Num. all: 34094 / Num. obs: 32867 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 93.3 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 99 Å / Redundancy: 3.54 % / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 93.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |