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Yorodumi- PDB-1h24: CDK2/CyclinA in complex with a 9 residue recruitment peptide from E2F -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h24 | ||||||
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Title | CDK2/CyclinA in complex with a 9 residue recruitment peptide from E2F | ||||||
Components |
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Keywords | TRANSFERASE / CELL CYCLE / PROTEIN KINASE / CYCLIN / CDK2 / RECRUITMENT / PEPTIDE SPECIFICITY / SERINE/THREONINE-PROTEIN KINASE / ATP- BINDING / CELL DIVISION / MITOSIS / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information Rb-E2F complex / lens fiber cell apoptotic process / negative regulation of fat cell proliferation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / cyclin A2-CDK2 complex / cell cycle G1/S phase transition ...Rb-E2F complex / lens fiber cell apoptotic process / negative regulation of fat cell proliferation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / cyclin A2-CDK2 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / p53-Dependent G1 DNA Damage Response / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Regulation of APC/C activators between G1/S and early anaphase / Transcription of E2F targets under negative control by DREAM complex / cellular response to leptin stimulus / mRNA stabilization / male pronucleus / Telomere Extension By Telomerase / G0 and Early G1 / female pronucleus / Activation of NOXA and translocation to mitochondria / anoikis / response to glucagon / cellular response to cocaine / cellular response to nitric oxide / cyclin-dependent protein serine/threonine kinase regulator activity / Activation of PUMA and translocation to mitochondria / cellular response to insulin-like growth factor stimulus / Cyclin E associated events during G1/S transition / DNA-binding transcription activator activity / positive regulation of DNA biosynthetic process / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cochlea development / negative regulation of fat cell differentiation / G1/S-Specific Transcription / cellular response to platelet-derived growth factor stimulus / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of DNA binding / cyclin-dependent protein kinase holoenzyme complex / Transcriptional Regulation by E2F6 / regulation of DNA replication / regulation of G1/S transition of mitotic cell cycle / intrinsic apoptotic signaling pathway by p53 class mediator / animal organ regeneration / cis-regulatory region sequence-specific DNA binding / post-translational protein modification / forebrain development / cellular response to estradiol stimulus / DNA Damage/Telomere Stress Induced Senescence / DNA damage checkpoint signaling / CDK-mediated phosphorylation and removal of Cdc6 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Transcriptional regulation of granulopoiesis / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / Cyclin D associated events in G1 / Oncogene Induced Senescence / G1/S transition of mitotic cell cycle / RNA polymerase II transcription regulator complex / Pre-NOTCH Transcription and Translation / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / Regulation of TP53 Degradation / cellular response to xenobiotic stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / Oxidative Stress Induced Senescence / sequence-specific DNA binding / molecular adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA-binding transcription factor activity / positive regulation of apoptotic process / cell division / negative regulation of DNA-templated transcription / centrosome / DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 1h24.cif.gz | 236.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h24.ent.gz | 190.9 KB | Display | PDB format |
PDBx/mmJSON format | 1h24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h24_validation.pdf.gz | 473.9 KB | Display | wwPDB validaton report |
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Full document | 1h24_full_validation.pdf.gz | 535.1 KB | Display | |
Data in XML | 1h24_validation.xml.gz | 49.4 KB | Display | |
Data in CIF | 1h24_validation.cif.gz | 68.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/1h24 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/1h24 | HTTPS FTP |
-Related structure data
Related structure data | 1h25C 1h26C 1h27C 1h28C 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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Details | BIOMOLECULE 1 IS A TRIMERIC COMPLEX OF CHAINS A, B AND E. BIOMOLECULE 2 IS A DIMERIC COMPLEX OF CHAINS C AND D |
-Components
#1: Protein | Mass: 34467.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PHOSPHORYLATED ON THR160 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Protein | Mass: 29753.410 Da / Num. of mol.: 2 / Fragment: CYCLIN FOLD FRAGMENT, 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: 1128.345 Da / Num. of mol.: 1 / Fragment: RESIDUES 87-95 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q01094 #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. E2F: TRANSCRIPT | Sequence details | CHAINS B AND D ARE A TRUNCATED FRAGMENT OF CYCLIN A2 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 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→28.8 Å / Num. obs: 48503 / % possible obs: 95.6 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 1.7 / % possible all: 94.4 |
Reflection | *PLUS Num. measured all: 124102 |
Reflection shell | *PLUS % possible obs: 94.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QMZ Resolution: 2.5→28.8 Å / SU B: 14.242 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R: 0.542 / ESU R Free: 0.313
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Displacement parameters | Biso mean: 55.703 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→28.8 Å
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Refinement | *PLUS Lowest resolution: 100 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.212 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.56 Å / Rfactor Rfree: 0.345 / Rfactor Rwork: 0.264 / Num. reflection Rwork: 173 / Total num. of bins used: 20 |