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Yorodumi- PDB-2cci: Crystal structure of phospho-CDK2 Cyclin A in complex with a pept... -
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-Basic information
Entry | Database: PDB / ID: 2cci | ||||||
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Title | Crystal structure of phospho-CDK2 Cyclin A in complex with a peptide containing both the substrate and recruitment sites of CDC6 | ||||||
Components |
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Keywords | CELL CYCLE / COMPLEX (TRANSFERASE-CELL DIVISION) / PROTEIN KINASES / RECRUITMENT / SUBSTRATE RECOGNITION / ATP-BINDING / CELL DIVISION / KINASE / MITOSIS / NUCLEOTIDE-BINDING / PHOSPHORYLATION / SERINE/THREONINE- PROTEIN KINASE / TRANSFERASE / CYCLIN / DNA REPLICATION / NUCLEAR PROTEIN / COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of chromosome segregation / cellular response to vasopressin / CDC6 association with the ORC:origin complex / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / traversing start control point of mitotic cell cycle / DNA replication checkpoint signaling / mitotic cell cycle phase transition ...positive regulation of chromosome segregation / cellular response to vasopressin / CDC6 association with the ORC:origin complex / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / traversing start control point of mitotic cell cycle / DNA replication checkpoint signaling / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by DREAM complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / mitotic DNA replication checkpoint signaling / male pronucleus / female pronucleus / cellular response to angiotensin / regulation of mitotic metaphase/anaphase transition / response to glucagon / cellular response to cocaine / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / intercellular bridge / G1/S-Specific Transcription / cochlea development / negative regulation of DNA replication / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to platelet-derived growth factor stimulus / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / positive regulation of cytokinesis / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of anaphase-promoting complex-dependent catabolic process / regulation of DNA replication / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / DNA replication initiation / G0 and Early G1 / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / spindle midzone / Cajal body / animal organ regeneration / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Activation of ATR in response to replication stress / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / meiotic cell cycle / male germ cell nucleus / response to organic substance / cellular response to estradiol stimulus / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / G1/S transition of mitotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / mitotic spindle / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / kinase binding / spindle pole / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / positive regulation of fibroblast proliferation / G2/M transition of mitotic cell cycle / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / Ras protein signal transduction Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Cheng, K.Y. / Noble, M.E.M. / Skamnaki, V. / Brown, N.R. / Lowe, E.D. / Kontogiannis, L. / Shen, K. / Cole, P.A. / Siligardi, G. / Johnson, L.N. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2006 Title: The role of the phospho-CDK2/cyclin A recruitment site in substrate recognition. Authors: Cheng, K.Y. / Noble, M.E. / Skamnaki, V. / Brown, N.R. / Lowe, E.D. / Kontogiannis, L. / Shen, K. / Cole, P.A. / Siligardi, G. / Johnson, L.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cci.cif.gz | 240.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cci.ent.gz | 192 KB | Display | PDB format |
PDBx/mmJSON format | 2cci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/2cci ftp://data.pdbj.org/pub/pdb/validation_reports/cc/2cci | HTTPS FTP |
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-Related structure data
Related structure data | 2cchC 1qmzS 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 , 2 types, 4 molecules ACBD
#1: Protein | Mass: 34143.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PHOSPHORYLATED AT RESIDUE T160 / Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P24941, cyclin-dependent kinase #2: Protein | Mass: 29624.297 Da / Num. of mol.: 2 / Fragment: RESIDUES 175-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Plasmid: PET21D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P20248 |
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-Protein/peptide , 1 types, 2 molecules FI
#3: Protein/peptide | Mass: 3440.896 Da / Num. of mol.: 2 / Fragment: RESIDUES 71-100 / Mutation: YES / Source method: obtained synthetically / Details: PEPTIDE MODIFIED TO GENERATE ACTIVE SITE SEQUENCE / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99741 |
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-Non-polymers , 3 types, 115 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | INVOLVED IN THE CONTROL OF THE CELL CYCLE ENGINEERED RESIDUE IN CHAIN F, PRO 71 TO HIS ENGINEERED ...INVOLVED IN THE CONTROL OF THE CELL CYCLE ENGINEERED |
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Sequence details | CHAINS B AND D ARE A TRUNCATED FRAGMENT OF CYCLIN A2 CONSISTING OF RESIDUES 175-432 THE PEPTIDE ...CHAINS B AND D ARE A TRUNCATED FRAGMENT OF CYCLIN A2 CONSISTING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % |
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Crystal grow | pH: 5.6 Details: 10-17% (V/V) PEG MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULPHATE AND 0.1 M MES PH 5.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. obs: 39629 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.7→2.85 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.2 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QMZ Resolution: 2.7→94.92 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.775 / SU B: 34.164 / SU ML: 0.347 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 12.217 / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→94.92 Å
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