+Open data
-Basic information
Entry | Database: PDB / ID: 3vu7 | ||||||
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Title | Crystal structure of REV1-REV7-REV3 ternary complex | ||||||
Components |
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Keywords | REPLICATION / DNA polymerase / DNA replication / Translesion DNA synthesis / DNA damage tolerance / DNA repair | ||||||
Function / homology | Function and homology information somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / deoxycytidyl transferase activity / telomere maintenance in response to DNA damage / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / deoxycytidyl transferase activity / telomere maintenance in response to DNA damage / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of epithelial to mesenchymal transition / JUN kinase binding / negative regulation of ubiquitin protein ligase activity / error-free translesion synthesis / mitotic spindle assembly checkpoint signaling / positive regulation of double-strand break repair via nonhomologous end joining / negative regulation of double-strand break repair via homologous recombination / error-prone translesion synthesis / positive regulation of epithelial to mesenchymal transition / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / actin filament organization / regulation of cell growth / Termination of translesion DNA synthesis / double-strand break repair via homologous recombination / negative regulation of canonical Wnt signaling pathway / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / DNA-templated DNA replication / spindle / double-strand break repair / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / positive regulation of peptidyl-serine phosphorylation / site of double-strand break / chromosome / 4 iron, 4 sulfur cluster binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cell division / nucleotide binding / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kikuchi, S. / Hara, K. / Shimizu, T. / Sato, M. / Hashimoto, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural basis of recruitment of DNA polymerase [zeta] by interaction between REV1 and REV7 proteins Authors: Kikuchi, S. / Hara, K. / Shimizu, T. / Sato, M. / Hashimoto, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vu7.cif.gz | 143 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vu7.ent.gz | 112.2 KB | Display | PDB format |
PDBx/mmJSON format | 3vu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/3vu7 ftp://data.pdbj.org/pub/pdb/validation_reports/vu/3vu7 | HTTPS FTP |
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-Related structure data
Related structure data | 3abdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 14095.096 Da / Num. of mol.: 1 / Fragment: UNP residues 1140-1251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REV1, REV1L / Production host: Escherichia coli (E. coli) References: UniProt: Q9UBZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Protein | Mass: 26101.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2L2, MAD2B, REV7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI95 |
#3: Protein | Mass: 5632.319 Da / Num. of mol.: 1 / Fragment: UNP residues 1847-1898 / Mutation: R124A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REV3L, POLZ, REV3 / Production host: Escherichia coli (E. coli) / References: UniProt: O60673, DNA-directed DNA polymerase |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.8 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
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Detector | Date: Jun 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→65.01 Å / Num. obs: 10306 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ABD Resolution: 2.8→65.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 31.343 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.143 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→65.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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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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