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Yorodumi- PDB-6hm5: Crystal structure of TOPBP1 BRCT0,1,2 in complex with a RAD9 phos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hm5 | ||||||
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Title | Crystal structure of TOPBP1 BRCT0,1,2 in complex with a RAD9 phosphopeptide | ||||||
Components |
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Keywords | CELL CYCLE / BRCT domain phosphopeptide recognition | ||||||
Function / homology | Function and homology information HDR through Single Strand Annealing (SSA) / Processing of DNA double-strand break ends / checkpoint clamp complex / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / HDR through Single Strand Annealing (SSA) ...HDR through Single Strand Annealing (SSA) / Processing of DNA double-strand break ends / checkpoint clamp complex / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / response to ionizing radiation / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / DNA replication initiation / Activation of ATR in response to replication stress / 3'-5' exonuclease activity / DNA damage checkpoint signaling / condensed nuclear chromosome / male germ cell nucleus / cellular response to ionizing radiation / G2/M DNA damage checkpoint / PML body / SH3 domain binding / histone deacetylase binding / intrinsic apoptotic signaling pathway in response to DNA damage / actin cytoskeleton / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA repair / DNA damage response / protein kinase binding / enzyme binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.33003812226 Å | ||||||
Authors | Day, M. / Rappas, M. / Oliver, A.W. / Pearl, L.H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Elife / Year: 2018 Title: BRCT domains of the DNA damage checkpoint proteins TOPBP1/Rad4 display distinct specificities for phosphopeptide ligands. Authors: Day, M. / Rappas, M. / Ptasinska, K. / Boos, D. / 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 | 6hm5.cif.gz | 129.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hm5.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 6hm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/6hm5 ftp://data.pdbj.org/pub/pdb/validation_reports/hm/6hm5 | HTTPS FTP |
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-Related 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: 33156.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: TOPBP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D5P3M9 |
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#2: Protein/peptide | Mass: 1212.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99638, exodeoxyribonuclease III |
#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: 2.21 Å3/Da / Density % sol: 44.31 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, sitting drop Details: 100 mM bicine/Trizma base pH 8.5, 300 mM diethyleneglycol, 300 mM triethyleneglycol, 300 mM tetraethyleneglycol, 300 mM pentaethyleneglycol, 10% w/v PEG 20000 and 20% v/v PEG MME 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91407 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91407 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→38.7 Å / Num. obs: 11242 / % possible obs: 98.97 % / Redundancy: 3 % / Biso Wilson estimate: 39.53 Å2 / Net I/σ(I): 9.72 |
Reflection shell | Resolution: 2.33→2.413 Å |
-Processing
Software |
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Refinement | Resolution: 2.33003812226→38.6991869814 Å / SU ML: 0.299558096022 / Cross valid method: FREE R-VALUE / σ(F): 1.34353251682 / Phase error: 24.5216819247
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.5979895974 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33003812226→38.6991869814 Å
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Refine LS restraints |
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LS refinement shell |
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