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Yorodumi- PDB-1gy3: pCDK2/cyclin A in complex with MgADP, nitrate and peptide substrate -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gy3 | |||||||||
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Title | pCDK2/cyclin A in complex with MgADP, nitrate and peptide substrate | |||||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE SUBSTRATE / TRANSFERASE-TRANSFERASE SUBSTRATE COMPLEX / CELL CYCLE REGULATORY PROTEIN KINASE / THR160-PHOSPHO-CYCLIN DEPENDENT PROTEIN KINASE 2 IN ASSOCIATION WITH CYCLIN A / TRANSFERASE- TRANSFERASE SUBSTRATE COMPLEX | |||||||||
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 / response to glucagon ...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 / 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 / cochlea development / 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 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 / G0 and Early G1 / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / 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 / 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 / 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 / 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 / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA replication / chromosome, telomeric region / Ub-specific processing proteases / endosome / chromatin remodeling / cell division / protein domain specific binding / protein phosphorylation / DNA repair / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / DNA-templated transcription / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / negative regulation of transcription by RNA polymerase II Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) SYNTHETIC CONSTRUCT (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Cook, A. / Lowe, E.D. / Chrysina, E.D. / Skamnaki, V.T. / Oikonomakos, N.G. / Johnson, L.N. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structural Studies on Phospho-Cdk2/Cyclin a Bound to Nitrate, a Transition State Analogue: Implications for the Protein Kinase Mechanism Authors: Cook, A. / Lowe, E.D. / Chrysina, E.D. / Skamnaki, V.T. / Oikonomakos, N.G. / Johnson, L.N. #1: Journal: Nat.Cell Biol. / Year: 1999 Title: The Structural Basis for Specificity of Substrate and Recruitment Peptides Fo Cyclin-Dependent 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 | 1gy3.cif.gz | 240.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gy3.ent.gz | 192.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/1gy3 ftp://data.pdbj.org/pub/pdb/validation_reports/gy/1gy3 | HTTPS FTP |
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-Related structure data
Related structure data | 1qmzS 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: (Code: given Matrix: (0.99995, 0.00733, -0.00605), Vector: |
-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 ON THR160 / Source: (gene. exp.) HOMO SAPIENS (human) Description: CDK2 WAS CO-EXPRESSED WITH CAK1 - PRODUCE THR160-PHOSPHO-CDK2 Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: P24941 #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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: P20248 |
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-Protein/peptide , 1 types, 2 molecules EF
#3: Protein/peptide | Mass: 835.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SEQUENCE HHASPRK / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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-Non-polymers , 5 types, 170 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | VAL B 175, N-TERMINAL DELETION OF RESIDUES 1-174 ENGINEERED IN EXPRESSION CONSTRUCT VAL D 175, N- ...VAL B 175, N-TERMINAL DELETION OF RESIDUES 1-174 ENGINEERED |
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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: 3.3 Å3/Da / Density % sol: 64.51 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 Details: CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 4C FROM SOLUTIONS CONTAINING 10 MG/ML PCDK2/CYCLIN A, 100 MM HEPES PH7.0, 2 MM SUBSTRATE PEPTIDE, 1MM ADP, 1.0 M LI2SO4. CRYSTALS WERE TRANSFERRED ...Details: CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 4C FROM SOLUTIONS CONTAINING 10 MG/ML PCDK2/CYCLIN A, 100 MM HEPES PH7.0, 2 MM SUBSTRATE PEPTIDE, 1MM ADP, 1.0 M LI2SO4. CRYSTALS WERE TRANSFERRED TO 20%PEG 8K, 100 MM HEPES PH 7.0, 10 MM SUBSSTRATE PEPTIDE, 5 MM MG(NO3)2 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 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: ID14-2 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 45572 / % possible obs: 84.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.7→2.81 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.5 / % possible all: 40.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 319218 |
Reflection shell | *PLUS % possible obs: 40.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QMZ Resolution: 2.7→20 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / ESU R Free: 0.42
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.25 / Rfactor Rwork: 0.25 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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