+Open data
-Basic information
Entry | Database: PDB / ID: 5c6d | ||||||
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Title | Crystal structure of USP7 in complex with UHRF1 | ||||||
Components |
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Keywords | HYDROLASE/LIGASE / USP7 / UHRF1 / HYDROLASE-LIGASE complex | ||||||
Function / homology | Function and homology information histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / regulation of telomere capping / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / hemi-methylated DNA-binding / deubiquitinase activity / homologous recombination ...histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / regulation of telomere capping / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / hemi-methylated DNA-binding / deubiquitinase activity / homologous recombination / DNA alkylation repair / regulation of epithelial cell proliferation / methyl-CpG binding / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic spindle assembly / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / transcription-coupled nucleotide-excision repair / heterochromatin / negative regulation of gluconeogenesis / heterochromatin formation / epigenetic regulation of gene expression / negative regulation of TORC1 signaling / methylated histone binding / positive regulation of protein metabolic process / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / regulation of signal transduction by p53 class mediator / replication fork / double-strand break repair via homologous recombination / euchromatin / RING-type E3 ubiquitin transferase / regulation of protein stability / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / PML body / nuclear matrix / spindle / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Regulation of TP53 Degradation / rhythmic process / p53 binding / chromosome / histone binding / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nucleic acid binding / nuclear body / protein stabilization / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / proteolysis / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.292 Å | ||||||
Authors | Zhang, Z.-M. / Song, J. | ||||||
Citation | Journal: Cell Rep / Year: 2015 Title: An Allosteric Interaction Links USP7 to Deubiquitination and Chromatin Targeting of UHRF1. Authors: Zhang, Z.M. / Rothbart, S.B. / Allison, D.F. / Cai, Q. / Harrison, J.S. / Li, L. / Wang, Y. / Strahl, B.D. / Wang, G.G. / Song, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c6d.cif.gz | 273 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c6d.ent.gz | 219.8 KB | Display | PDB format |
PDBx/mmJSON format | 5c6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c6d_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
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Full document | 5c6d_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 5c6d_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 5c6d_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/5c6d ftp://data.pdbj.org/pub/pdb/validation_reports/c6/5c6d | HTTPS FTP |
-Related structure data
Related structure data | 2ylmS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37361.305 Da / Num. of mol.: 2 / Fragment: UNP residues 561-881 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1 #2: Protein/peptide | Mass: 3381.789 Da / Num. of mol.: 2 / Fragment: UNP residues 634-665 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Production host: Escherichia coli (E. coli) References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #3: 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: 2.56 Å3/Da / Density % sol: 51.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 100 mM CHES (pH 9.0), 20% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9774 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 30, 2014 |
Radiation | Monochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→50 Å / Num. obs: 36467 / % possible obs: 98.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.64 |
Reflection shell | Resolution: 2.29→2.35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.2 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YLM Resolution: 2.292→49.251 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.292→49.251 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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