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Yorodumi- PDB-2fop: The Crystal Structure of the N-terminal domain of HAUSP/USP7 comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fop | ||||||
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Title | The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with mdm2 peptide 147-150 | ||||||
Components |
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Keywords | HYDROLASE / MATH Domain | ||||||
Function / homology | Function and homology information regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / deubiquitinase activity / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether ...regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / deubiquitinase activity / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / DNA alkylation repair / receptor serine/threonine kinase binding / Trafficking of AMPA receptors / positive regulation of vascular associated smooth muscle cell migration / regulation of DNA-binding transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / peroxisome proliferator activated receptor binding / response to iron ion / negative regulation of protein processing / K48-linked deubiquitinase activity / SUMO transferase activity / response to steroid hormone / NEDD8 ligase activity / symbiont-mediated disruption of host cell PML body / AKT phosphorylates targets in the cytosol / atrioventricular valve morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / endocardial cushion morphogenesis / negative regulation of NF-kappaB transcription factor activity / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / cellular response to alkaloid / blood vessel development / regulation of protein catabolic process / cardiac septum morphogenesis / protein deubiquitination / Constitutive Signaling by AKT1 E17K in Cancer / ligase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / response to magnesium ion / protein sumoylation / SUMOylation of transcription factors / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to UV-C / blood vessel remodeling / cellular response to estrogen stimulus / transcription-coupled nucleotide-excision repair / protein autoubiquitination / cellular response to actinomycin D / negative regulation of gluconeogenesis / ribonucleoprotein complex binding / negative regulation of TORC1 signaling / positive regulation of vascular associated smooth muscle cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / NPAS4 regulates expression of target genes / transcription repressor complex / regulation of heart rate / Regulation of PTEN localization / positive regulation of mitotic cell cycle / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / proteolysis involved in protein catabolic process / positive regulation of protein export from nucleus / regulation of signal transduction by p53 class mediator / response to cocaine / ubiquitin binding / Stabilization of p53 / Regulation of RUNX3 expression and activity / protein destabilization / RING-type E3 ubiquitin transferase / Signaling by ALK fusions and activated point mutants / establishment of protein localization / regulation of protein stability / Oncogene Induced Senescence / regulation of circadian rhythm / Regulation of TP53 Activity through Methylation / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / cellular response to gamma radiation / Formation of TC-NER Pre-Incision Complex / response to toxic substance / cellular response to growth factor stimulus / PML body / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / ubiquitin-protein transferase activity / endocytic vesicle membrane / ubiquitin protein ligase activity / disordered domain specific binding / Regulation of TP53 Degradation / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / negative regulation of neuron projection development / chromosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Saridakis, V. / Sheng, Y. / Sarkari, F. / Duan, S. / Wu, T. / Arrowsmith, C.H. / Frappier, L. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Molecular recognition of p53 and MDM2 by USP7/HAUSP Authors: Sheng, Y. / Saridakis, V. / Sarkari, F. / Duan, S. / Wu, T. / Arrowsmith, C.H. / Frappier, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fop.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fop.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 2fop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/2fop ftp://data.pdbj.org/pub/pdb/validation_reports/fo/2fop | HTTPS FTP |
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-Related structure data
Related structure data | 2fojC 2fooC 1yy6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18133.102 Da / Num. of mol.: 1 / Fragment: MATH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HAUSP, USP7 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93009, EC: 3.1.2.15 |
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#2: Protein/peptide | Mass: 634.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q00987*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG4K, 0.1 M Tris, 0.2 M Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 30, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 13054 / Num. obs: 10923 / Redundancy: 2.5 % / Biso Wilson estimate: 11.4 Å2 / Rsym value: 0.112 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2 / Rsym value: 0.543 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1YY6 Resolution: 2.1→19.9 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 170841.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.0416 Å2 / ksol: 0.371217 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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