+Open data
-Basic information
Entry | Database: PDB / ID: 6ath | ||||||
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Title | Cdk2/cyclin A/p27-KID-deltaC | ||||||
Components |
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Keywords | TRANSFERASE / Inhibitor / Complex / IDP / CDK / Cyclin / kinase / Phosphortlation | ||||||
Function / homology | Function and homology information cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / autophagic cell death / negative regulation of epithelial cell proliferation involved in prostate gland development / FOXO-mediated transcription of cell cycle genes / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition ...cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / autophagic cell death / negative regulation of epithelial cell proliferation involved in prostate gland development / FOXO-mediated transcription of cell cycle genes / 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 / regulation of cell cycle G1/S phase transition / regulation of exit from mitosis / epithelial cell proliferation involved in prostate gland development / mitotic cell cycle phase transition / negative regulation of epithelial cell apoptotic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of phosphorylation / ubiquitin ligase activator activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to leptin stimulus / RHO GTPases activate CIT / male pronucleus / female pronucleus / nuclear export / cellular response to cocaine / response to glucagon / AKT phosphorylates targets in the cytosol / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / Cul4A-RING E3 ubiquitin ligase complex / epithelial cell apoptotic process / cellular response to antibiotic / negative regulation of kinase activity / positive regulation of DNA biosynthetic process / cochlea development / molecular function inhibitor activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cellular response to platelet-derived growth factor stimulus / cyclin E1-CDK2 complex / protein kinase inhibitor activity / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cellular response to lithium ion / 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 cyclin-dependent protein serine/threonine kinase activity / Constitutive Signaling by AKT1 E17K in Cancer / regulation of G1/S transition of mitotic cell cycle / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of vascular associated smooth muscle cell proliferation / inner ear development / regulation of DNA replication / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / negative regulation of mitotic cell cycle / cellular response to organic cyclic compound / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / response to amino acid / animal organ regeneration / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / localization / response to glucose / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cajal body / response to cadmium ion / 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 / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Cyclin A:Cdk2-associated events at S phase entry / regulation of cell migration / condensed chromosome / positive regulation of microtubule polymerization / Notch signaling pathway / mitotic G1 DNA damage checkpoint signaling / Hsp70 protein binding / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / FLT3 Signaling / cyclin binding / post-translational protein modification / meiotic cell cycle / placenta development Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | White, S.W. / Yun, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation. Authors: Tsytlonok, M. / Sanabria, H. / Wang, Y. / Felekyan, S. / Hemmen, K. / Phillips, A.H. / Yun, M.K. / Waddell, M.B. / Park, C.G. / Vaithiyalingam, S. / Iconaru, L. / White, S.W. / Tompa, P. / ...Authors: Tsytlonok, M. / Sanabria, H. / Wang, Y. / Felekyan, S. / Hemmen, K. / Phillips, A.H. / Yun, M.K. / Waddell, M.B. / Park, C.G. / Vaithiyalingam, S. / Iconaru, L. / White, S.W. / Tompa, P. / Seidel, C.A.M. / Kriwacki, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ath.cif.gz | 260.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ath.ent.gz | 207.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ath.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/6ath ftp://data.pdbj.org/pub/pdb/validation_reports/at/6ath | HTTPS FTP |
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-Related structure data
Related structure data | 1jsuS 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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Unit cell |
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-Components
#1: Protein | Mass: 34200.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Phosphorylated / Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Protein | Mass: 30142.834 Da / Num. of mol.: 1 / Fragment: UNP residues 173-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P20248 |
#3: Protein | Mass: 8105.980 Da / Num. of mol.: 1 / Fragment: UNP residues 22-85 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDKN1B, KIP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P46527 |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: HEPES, Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2007 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. obs: 71452 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6848 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JSU Resolution: 1.82→29.625 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.44
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 42.912 Å2 / ksol: 0.377 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→29.625 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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