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Yorodumi- PDB-1h26: CDK2/CyclinA in complex with an 11-residue recruitment peptide fr... -
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-Basic information
Entry | Database: PDB / ID: 1h26 | ||||||
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Title | CDK2/CyclinA in complex with an 11-residue recruitment peptide from p53 | ||||||
Components |
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Keywords | CELL CYCLE / PROTEIN KINASE / CYCLIN / CDK2 / RECRUITMENT / PEPTIDE SPECIFICITY | ||||||
Function / homology | Function and homology information 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 / cellular response to leptin stimulus / male pronucleus / female pronucleus / Loss of function of TP53 in cancer due to loss of tetramerization ability ...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 / cellular response to leptin stimulus / male pronucleus / female pronucleus / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / cellular response to cocaine / response to glucagon / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / cyclin-dependent protein serine/threonine kinase regulator activity / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / cellular response to insulin-like growth factor stimulus / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / positive regulation of DNA biosynthetic process / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / positive regulation of execution phase of apoptosis / cochlea development / negative regulation of DNA replication / ER overload response / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to platelet-derived growth factor stimulus / cyclin A2-CDK2 complex / B cell lineage commitment / positive regulation of DNA-templated DNA replication initiation / G2 Phase / thymocyte apoptotic process / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of cardiac muscle cell apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / T cell proliferation involved in immune response / cardiac septum morphogenesis / X chromosome / PTK6 Regulates Cell Cycle / entrainment of circadian clock by photoperiod / regulation of DNA replication / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / regulation of anaphase-promoting complex-dependent catabolic process / Zygotic genome activation (ZGA) / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / necroptotic process / rRNA transcription / positive regulation of release of cytochrome c from mitochondria / centriole replication / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / Regulation of APC/C activators between G1/S and early anaphase / TFIID-class transcription factor complex binding / centrosome duplication / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / general transcription initiation factor binding / intrinsic apoptotic signaling pathway by p53 class mediator Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 | 1h26.cif.gz | 233.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h26.ent.gz | 187.4 KB | Display | PDB format |
PDBx/mmJSON format | 1h26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/1h26 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/1h26 | HTTPS FTP |
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-Related structure data
Related structure data | 1h24C 1h25C 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, 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: 1367.682 Da / Num. of mol.: 1 / Fragment: RESIDUES 376-386 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P04637 #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. P53: 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: 3.1 Å3/Da / Density % sol: 59.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: BM14 / Wavelength: 0.9537 |
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: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→29.88 Å / Num. obs: 63733 / % possible obs: 96.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.24→2.36 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.3 / % possible all: 75.5 |
Reflection | *PLUS Highest resolution: 2.24 Å / Lowest resolution: 29.88 Å / Num. measured all: 223072 / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS % possible obs: 75.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QMZ Resolution: 2.24→29.88 Å / SU B: 15.477 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R Free: 0.231
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Displacement parameters | Biso mean: 44.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→29.88 Å
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Refinement | *PLUS Highest resolution: 2.24 Å / Lowest resolution: 29.88 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.244 Å / Lowest resolution: 2.302 Å / Rfactor Rfree: 0.381 / Rfactor Rwork: 0.253 / Num. reflection Rwork: 168 / Total num. of bins used: 20 |