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Yorodumi- PDB-6k07: Crystal structure of REV7(R124A) in complex with a Shieldin3 fragment -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k07 | ||||||
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Title | Crystal structure of REV7(R124A) in complex with a Shieldin3 fragment | ||||||
Components |
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Keywords | TRANSCRIPTION/PROTEIN BINDING / DSB repair complex / GENE REGULATION / TRANSCRIPTION-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / telomere maintenance in response to DNA damage / 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 / JUN kinase binding ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / telomere maintenance in response to DNA damage / 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 / JUN kinase binding / negative regulation of epithelial to mesenchymal transition / negative regulation of ubiquitin protein ligase activity / 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 / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / actin filament organization / negative regulation of protein catabolic process / regulation of cell growth / negative regulation of canonical Wnt signaling pathway / negative regulation of DNA-binding transcription factor activity / spindle / chromosome / positive regulation of peptidyl-serine phosphorylation / double-strand break repair / site of double-strand break / RNA polymerase II-specific DNA-binding transcription factor binding / cell division / DNA repair / positive regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Zhang, F. / Dai, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structural basis for shieldin complex subunit 3-mediated recruitment of the checkpoint protein REV7 during DNA double-strand break repair. Authors: Dai, Y. / Zhang, F. / Wang, L. / Shan, S. / Gong, Z. / Zhou, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k07.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k07.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 6k07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/6k07 ftp://data.pdbj.org/pub/pdb/validation_reports/k0/6k07 | HTTPS FTP |
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-Related structure data
Related structure data | 6k08C 3abdS S: Starting model for refinement C: citing same article (ref.) |
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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: 25195.188 Da / Num. of mol.: 1 / Mutation: R124A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2L2, MAD2B, REV7 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9UI95 |
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#2: Protein/peptide | Mass: 3358.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SHLD3, FLJ26957, RINN1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q6ZNX1 |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.53 Å3/Da / Density % sol: 51.33 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate, Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→49.16 Å / Num. obs: 14467 / % possible obs: 99.8 % / Redundancy: 9.5 % / Rpim(I) all: 0.021 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.23→2.3 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 13263 / Rpim(I) all: 0.505 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ABD Resolution: 2.24→49.16 Å / Cross valid method: FREE R-VALUE
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→49.16 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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