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Yorodumi- PDB-5o8k: Crystal structure of mammalian Rev7 in complex with Rev3 1875-1895 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o8k | ||||||
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Title | Crystal structure of mammalian Rev7 in complex with Rev3 1875-1895 | ||||||
Components |
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Keywords | REPLICATION / Rev7 / Mad2L2 / DNA Polymerase zeta / DNA replication | ||||||
Function / homology | Function and homology information Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / telomere maintenance in response to DNA damage / zeta DNA polymerase complex / anaphase-promoting complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly ...Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / telomere maintenance in response to DNA damage / zeta DNA polymerase complex / anaphase-promoting complex / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of epithelial to mesenchymal transition / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / negative regulation of ubiquitin protein ligase activity / negative regulation of double-strand break repair via homologous recombination / positive regulation of double-strand break repair via nonhomologous end joining / positive regulation of epithelial to mesenchymal transition / error-prone translesion synthesis / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / actin filament organization / regulation of cell growth / double-strand break repair via homologous recombination / negative regulation of canonical Wnt signaling pathway / negative regulation of protein catabolic process / DNA-templated DNA replication / spindle / double-strand break repair / positive regulation of peptidyl-serine phosphorylation / site of double-strand break / 4 iron, 4 sulfur cluster binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cell cycle / cell division / nucleotide binding / chromatin / positive regulation of gene expression / 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 | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Emamzadah, S. / Tropia, L. / Huber, F. / Halazonetis, T. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: Crystal structure of mammalian Rev7 in complex with Rev3 1875-1895 Authors: Emamzadah, S. / Tropia, L. / Huber, F. / Halazonetis, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o8k.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o8k.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 5o8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/5o8k ftp://data.pdbj.org/pub/pdb/validation_reports/o8/5o8k | 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24473.545 Da / Num. of mol.: 1 / Mutation: F11S, G12A, V132K, C133V, A135K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mad2l2, Mad2b, Rev7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q9D752 |
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#2: Protein/peptide | Mass: 3141.685 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REV3L, POLZ, REV3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O60673, DNA-directed DNA polymerase |
#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: 2.13 Å3/Da / Density % sol: 42.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 2000 MME, 0.8M sodium formate, 0.1M tris-HCl pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9334 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→70 Å / Num. obs: 20408 / % possible obs: 96.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.071 / Rrim(I) all: 0.139 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3080 / Rpim(I) all: 0.166 / Rrim(I) all: 0.362 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Starting model: 3ABD Resolution: 1.8→70 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.8→70 Å
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