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Yorodumi- PDB-6rml: Crystal structure of TOPBP1 BRCT0,1,2 in complex with a 53BP1 pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rml | ||||||
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Title | Crystal structure of TOPBP1 BRCT0,1,2 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 / chromatin-protein adaptor activity / positive regulation of isotype switching / 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 / chromatin-protein adaptor activity / positive regulation of isotype switching / 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 / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA metabolic process / 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 / methylated histone binding / histone reader activity / protein serine/threonine kinase activator activity / condensed nuclear chromosome / replication fork / DNA damage checkpoint signaling / male germ cell nucleus / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / protein homooligomerization / 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 / chromosome, telomeric region / damaged DNA binding / 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: 2.81 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 | 6rml.cif.gz | 125.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rml.ent.gz | 97.8 KB | Display | PDB format |
PDBx/mmJSON format | 6rml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rml_validation.pdf.gz | 443.4 KB | Display | wwPDB validaton report |
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Full document | 6rml_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 6rml_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 6rml_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/6rml ftp://data.pdbj.org/pub/pdb/validation_reports/rm/6rml | HTTPS FTP |
-Related structure data
Related structure data | 6rmmC 2xnhS 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: 33891.410 Da / Num. of mol.: 2 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: 1755.701 Da / Num. of mol.: 1 / 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: 3.33 Å3/Da / Density % sol: 63.09 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, sitting drop Details: 10% w/v PEG 20 000 20% v/v PEG MME 550 0.03 M of each ethylene glycol 0.1 M MES/imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→69.55 Å / Num. obs: 23386 / % possible obs: 100 % / Redundancy: 4.9 % / Net I/σ(I): 17.91 |
Reflection shell | Resolution: 2.81→2.91 Å / Num. unique obs: 2287 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XNH Resolution: 2.81→69.55 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→69.55 Å
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Refine LS restraints |
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LS refinement shell |
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