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Yorodumi- PDB-1h28: CDK2/CyclinA in complex with an 11-residue recruitment peptide fr... -
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-Basic information
Entry | Database: PDB / ID: 1h28 | ||||||
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Title | CDK2/CyclinA in complex with an 11-residue recruitment peptide from p107 | ||||||
Components |
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Keywords | CELL CYCLE/TRANSFERASE SUBSTRATE / CELL CYCLE / PROTEIN KINASE / CYCLIN / CDK2 / RECRUITMENT / PEPTIDE SPECIFICITY / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / CELL DIVISION / MITOSIS / PHOSPHORYLATION / CELL CYCLE-TRANSFERASE SUBSTRATE / CELL CYCLE-TRANSFERASE SUBSTRATE COMPLEX | ||||||
Function / homology | Function and homology information regulation of lipid kinase activity / 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 / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / cellular response to leptin stimulus / male pronucleus ...regulation of lipid kinase activity / 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 / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / negative regulation of G1/S transition of mitotic cell cycle / cochlea development / G1/S-Specific Transcription / 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 / regulation of DNA replication / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of cellular senescence / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cajal body / Activation of ATR in response to replication stress / 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 mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / : / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / cellular response to estradiol stimulus / promoter-specific chromatin binding / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / G1/S transition of mitotic cell cycle / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / cellular senescence / positive regulation of fibroblast proliferation / Regulation of TP53 Degradation / nuclear envelope / chromatin organization / 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 / Regulation of TP53 Activity through Phosphorylation / DNA replication / Ras protein signal transduction / transcription regulator complex / chromosome, telomeric region / cell differentiation / Ub-specific processing proteases / endosome / chromatin remodeling Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Tews, I. / Cheng, K.Y. / Lowe, E.D. / Noble, M.E.M. / Brown, N.R. / Gul, S. / Gamblin, S. / Johnson, L.N. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Specificity Determinants of Recruitment Peptides Bound to Phospho-Cdk2/Cyclin A Authors: Lowe, E.D. / Tews, I. / Cheng, K.Y. / Brown, N.R. / Gul, S. / Noble, M.E.M. / Gamblin, S. / Johnson, L.N. #1: Journal: Nat.Cell Biol. / Year: 1999 Title: The Structural Basis for Specificity of Substrate and Recruitment Peptides for Cyclin-Dependant Kinases Authors: Brown, N.R. / Noble, M.E.M. / Endicott, J.A. / 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 | 1h28.cif.gz | 235.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h28.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 1h28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/1h28 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/1h28 | HTTPS FTP |
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-Related structure data
Related structure data | 1h24C 1h25C 1h26C 1h27C 1qmzS 1h0u C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 34467.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P24941 #2: Protein | Mass: 29753.410 Da / Num. of mol.: 2 / Fragment: CYCLIN FOLD, RESIDUES 175-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET21D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P20248 #3: Protein/peptide | Mass: 1194.365 Da / Num. of mol.: 2 / Fragment: RB PEPTIDE, RESIDUES 653-663 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P28749 #4: Water | ChemComp-HOH / | Compound details | CDK2: CONTROL OF THE CELL CYCLE DURING S PHASE AND G2. BELONGS TO THE SER/THR FAMILY OF PROTEIN ...CDK2: CONTROL OF THE CELL CYCLE DURING S PHASE AND G2. BELONGS TO THE SER/THR FAMILY OF PROTEIN KINASES. CYCLIN A2: CONTROL OF THE CELL CYCLE. INTERACTS WITH THE CDK2 AND CDC2 PROTEIN KINASES. P107: INVOLVED IN G1 ARREST. | Sequence details | MOLECULE IS A TRUNCATED FRAGMENT OF CYCLIN A3 CONSISTING | |
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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: 3.6 Å3/Da / Density % sol: 65.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 0.8M KCL, 1.2M (NH4)2SO4, 40MM HEPES PH 7.0. PROTEIN CONCENTRATION = 10MG/ML | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→28.99 Å / Num. obs: 41507 / % possible obs: 95.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 1.2 / % possible all: 97.8 |
Reflection | *PLUS Num. measured all: 92651 |
Reflection shell | *PLUS % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QMZ Resolution: 2.8→29.62 Å / SU B: 13.287 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 1.245 / ESU R Free: 0.45
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Displacement parameters | Biso mean: 30.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→29.62 Å
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 29.6 Å / Rfactor Rfree: 0.327 / Rfactor Rwork: 0.266 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.872 Å / Rfactor Rfree: 0.398 / Num. reflection Rfree: 141 / Rfactor Rwork: 0.302 / Num. reflection Rwork: 2950 / Total num. of bins used: 20 |