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Yorodumi- PDB-7ako: Crystal structure of CHK1 kinase domain in complex with a CLASPIN... -
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-Basic information
Entry | Database: PDB / ID: 7ako | |||||||||
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Title | Crystal structure of CHK1 kinase domain in complex with a CLASPIN phosphopeptide | |||||||||
Components |
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Keywords | CELL CYCLE | |||||||||
Function / homology | Function and homology information DNA secondary structure binding / anaphase-promoting complex binding / negative regulation of G0 to G1 transition / DNA replication checkpoint signaling / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic DNA replication checkpoint signaling / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division ...DNA secondary structure binding / anaphase-promoting complex binding / negative regulation of G0 to G1 transition / DNA replication checkpoint signaling / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic DNA replication checkpoint signaling / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / Activation of ATR in response to replication stress / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic / activation of protein kinase activity / nucleus organization / cellular response to caffeine / Apoptotic cleavage of cellular proteins / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / condensed nuclear chromosome / replicative senescence / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of cell cycle / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / replication fork / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / G2/M DNA damage checkpoint / cellular response to mechanical stimulus / Signaling by SCF-KIT / G2/M transition of mitotic cell cycle / Processing of DNA double-strand break ends / peptidyl-serine phosphorylation / regulation of cell population proliferation / DNA replication / Regulation of TP53 Activity through Phosphorylation / chromatin remodeling / non-specific serine/threonine protein kinase / protein kinase activity / Ub-specific processing proteases / protein domain specific binding / protein phosphorylation / intracellular membrane-bounded organelle / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / chromatin / apoptotic process / Golgi apparatus / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Day, M. / Oliver, A.W. / Pearl, L.H. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Structure / Year: 2021 Title: Structural basis for recruitment of the CHK1 DNA damage kinase by the CLASPIN scaffold protein. Authors: Day, M. / Parry-Morris, S. / Houghton-Gisby, J. / 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 | 7ako.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ako.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ako.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ako_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7ako_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7ako_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 7ako_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/7ako ftp://data.pdbj.org/pub/pdb/validation_reports/ak/7ako | HTTPS FTP |
-Related structure data
Related structure data | 7akmC 1ia8S 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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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 34357.352 Da / Num. of mol.: 2 / Mutation: D10R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK1, CHK1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O14757, non-specific serine/threonine protein kinase #2: Protein/peptide | Mass: 1896.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9HAW4 |
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-Non-polymers , 4 types, 324 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.59 Å3/Da / Density % sol: 52.47 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, sitting drop Details: 200 mM Sodium citrate tribasic dihydrate, 100 mM Bis-Tris propane pH 6.5 and 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96864 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→96.49 Å / Num. obs: 65068 / % possible obs: 96.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 29.03 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.8→1.84 Å / Num. unique obs: 2602 / CC1/2: 0.161 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IA8 Resolution: 1.8→96.49 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5014 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: 40.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→96.49 Å
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Refine LS restraints |
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LS refinement shell |
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