+Open data
-Basic information
Entry | Database: PDB / ID: 6kto | ||||||
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Title | Crystal structure of human SHLD3-C-REV7-O-REV7-SHLD2 complex | ||||||
Components |
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Keywords | REPLICATION / Shieldin / Complex / Conformational dimer / NHEJ | ||||||
Function / homology | Function and homology information somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / 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 epithelial to mesenchymal transition / 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 / 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 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 / regulation of double-strand break repair via homologous recombination / 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 / regulation of cell growth / negative regulation of canonical Wnt signaling pathway / negative regulation of DNA-binding transcription factor activity / negative regulation of protein catabolic process / spindle / double-strand break repair / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / site of double-strand break / chromosome / RNA polymerase II-specific DNA-binding transcription factor binding / cell division / DNA repair / chromatin / nucleolus / positive regulation of DNA-templated transcription / 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: 3.44976331487 Å | ||||||
Authors | Liang, L. / Yin, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Molecular basis for assembly of the shieldin complex and its implications for NHEJ. Authors: Liang, L. / Feng, J. / Zuo, P. / Yang, J. / Lu, Y. / Yin, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kto.cif.gz | 114.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kto.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 6kto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/6kto ftp://data.pdbj.org/pub/pdb/validation_reports/kt/6kto | HTTPS FTP |
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-Related structure data
Related structure data | 3vu7S 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: 26187.352 Da / Num. of mol.: 2 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 #2: Protein | | Mass: 7402.546 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 (E. coli) / References: UniProt: Q6ZNX1 #3: Protein | | Mass: 5953.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SHLD2, FAM35A, RINN2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86V20 |
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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: 3.15 Å3/Da / Density % sol: 60.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.02M Magnesium chloride hexahydrate, 0.1M HEPES 7.5, 22% w/v Poly (acrylic acid sodium salt) 5100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 3.44→50 Å / Num. obs: 11237 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 58.7354852027 Å2 / Rpim(I) all: 0.058 / Net I/σ(I): 12.75 |
Reflection shell | Resolution: 3.45→3.72 Å / Num. unique obs: 2312 / Rpim(I) all: 0.452 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3vu7 Resolution: 3.44976331487→46.4411009446 Å / SU ML: 0.408163546905 / Cross valid method: FREE R-VALUE / σ(F): 1.36702633773 / Phase error: 24.9565654608 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.6481043069 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.44976331487→46.4411009446 Å
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Refine LS restraints |
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LS refinement shell |
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