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Yorodumi- PDB-6rmm: Crystal structure of TOPBP1 BRCT4,5 in complex with a 53BP1 phosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rmm | ||||||
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Title | Crystal structure of TOPBP1 BRCT4,5 in complex with a 53BP1 phosphopeptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / BRCT domain Phosphopeptide recognition | ||||||
Function / homology | Function and homology information broken chromosome clustering / BRCA1-B complex / ubiquitin-modified histone reader activity / phosphorylation-dependent protein binding / positive regulation of isotype switching / chromatin-protein adaptor activity / cellular response to X-ray / homologous recombination / DNA replication checkpoint signaling / double-strand break repair via classical nonhomologous end joining ...broken chromosome clustering / BRCA1-B complex / ubiquitin-modified histone reader activity / phosphorylation-dependent protein binding / positive regulation of isotype switching / chromatin-protein adaptor activity / cellular response to X-ray / homologous recombination / DNA replication checkpoint signaling / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / mitotic DNA replication checkpoint signaling / DNA repair complex / DNA metabolic process / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / response to ionizing radiation / telomeric DNA binding / double-strand break repair via alternative nonhomologous end joining / mitotic G2 DNA damage checkpoint signaling / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / SUMOylation of transcription factors / DNA replication initiation / chromosome organization / negative regulation of double-strand break repair via homologous recombination / histone reader activity / methylated histone binding / protein serine/threonine kinase activator activity / condensed nuclear chromosome / DNA damage checkpoint signaling / replication fork / male germ cell nucleus / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / double-strand break repair via homologous recombination / protein homooligomerization / G2/M DNA damage checkpoint / PML body / kinetochore / positive regulation of DNA-binding transcription factor activity / spindle pole / double-strand break repair via nonhomologous end joining / p53 binding / actin cytoskeleton / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / site of double-strand break / Processing of DNA double-strand break ends / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA repair / centrosome / DNA damage response / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53 Å | ||||||
Authors | Day, M. / Oliver, A.W. / Pearl, L.H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Elife / Year: 2019 Title: Phosphorylation-mediated interactions with TOPBP1 couple 53BP1 and 9-1-1 to control the G1 DNA damage checkpoint. Authors: Bigot, N. / Day, M. / Baldock, R.A. / Watts, F.Z. / Oliver, A.W. / Pearl, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rmm.cif.gz | 160.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rmm.ent.gz | 128.6 KB | Display | PDB format |
PDBx/mmJSON format | 6rmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/6rmm ftp://data.pdbj.org/pub/pdb/validation_reports/rm/6rmm | HTTPS FTP |
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-Related structure data
Related structure data | 6rmlC 3uenS 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: 21507.539 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOPBP1, KIAA0259 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92547 #2: Protein/peptide | Mass: 1630.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12888*PLUS |
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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: 4.45 Å3/Da / Density % sol: 72.37 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, sitting drop Details: 10% w/v PEG 4000, 20% v/v glycerol 0.02 M of each carboxylic acid 0.1 M MOPS/HEPES-Na pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 3.53→67.405 Å / Num. obs: 20816 / % possible obs: 100 % / Redundancy: 70.6 % / Net I/σ(I): 21.03 |
Reflection shell | Resolution: 3.53→3.656 Å / Num. unique obs: 2034 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UEN Resolution: 3.53→67.405 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.53→67.405 Å
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Refine LS restraints |
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LS refinement shell |
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