+Open data
-Basic information
Entry | Database: PDB / ID: 1jow | ||||||
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Title | Crystal structure of a complex of human CDK6 and a viral cyclin | ||||||
Components |
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Keywords | CELL CYCLE/TRANSFERASE / CDK-cyclin complex / cyclin fold / CELL CYCLE-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information cyclin D2-CDK6 complex / cyclin D3-CDK6 complex / cyclin D1-CDK6 complex / cell dedifferentiation / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / FBXO family protein binding / lateral ventricle development / negative regulation of myeloid cell differentiation ...cyclin D2-CDK6 complex / cyclin D3-CDK6 complex / cyclin D1-CDK6 complex / cell dedifferentiation / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / FBXO family protein binding / lateral ventricle development / negative regulation of myeloid cell differentiation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / type B pancreatic cell development / negative regulation of monocyte differentiation / astrocyte development / dentate gyrus development / gliogenesis / regulation of cell motility / cyclin-dependent kinase / Regulation of RUNX1 Expression and Activity / cyclin-dependent protein serine/threonine kinase activity / regulation of hematopoietic stem cell differentiation / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of cell-matrix adhesion / negative regulation of osteoblast differentiation / generation of neurons / cyclin-dependent protein kinase holoenzyme complex / regulation of G2/M transition of mitotic cell cycle / negative regulation of cellular senescence / negative regulation of cell differentiation / : / negative regulation of cell cycle / cyclin binding / hematopoietic stem cell differentiation / Notch signaling pathway / ruffle / response to virus / regulation of erythrocyte differentiation / Cyclin D associated events in G1 / Oncogene Induced Senescence / G1/S transition of mitotic cell cycle / positive regulation of fibroblast proliferation / negative regulation of epithelial cell proliferation / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / T cell differentiation in thymus / Oxidative Stress Induced Senescence / regulation of cell cycle / protein phosphorylation / cell division / negative regulation of cell population proliferation / protein serine kinase activity / centrosome / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saimiriine herpesvirus 2 (Herpesvirus saimiri) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Schulze-Gahmen, U. / Kim, S.H. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Structural basis for CDK6 activation by a virus-encoded cyclin. Authors: Schulze-Gahmen, U. / Kim, S.H. #1: Journal: To be Published Title: Crystallization of a Complex between Human CDK6 and a Virus-encoded Cyclin is Critically Dependent on the Addition of Small Charged Organic Molecules Authors: Schulze-Gahmen, U. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jow.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jow.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jow_validation.pdf.gz | 432.6 KB | Display | wwPDB validaton report |
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Full document | 1jow_full_validation.pdf.gz | 463.3 KB | Display | |
Data in XML | 1jow_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 1jow_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/1jow ftp://data.pdbj.org/pub/pdb/validation_reports/jo/1jow | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | The biological assembly is the heterodimer in the asymmetric unit |
-Components
#1: Protein | Mass: 28665.416 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saimiriine herpesvirus 2 (Herpesvirus saimiri) Genus: Rhadinovirus / Plasmid: pFastBac HTa donor plasmid / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01043 |
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#2: Protein | Mass: 35066.332 Da / Num. of mol.: 1 / Fragment: residues 1-308 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK6 / Plasmid: pFastBac1 donor plasmid / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q00534, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.78 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris/HCL, sodium chloride, PEG 3350, calcium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 KDetails: Schulze-Gahmen, U., (2001) Acta Crystallogr, D57, 1287. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 17, 2000 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. all: 12815 / Num. obs: 12783 / % possible obs: 0.98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Rsym value: 0.057 / Net I/σ(I): 29 |
Reflection shell | Resolution: 3.1→3.19 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.29 / % possible all: 0.82 |
Reflection | *PLUS Num. obs: 12678 / % possible obs: 97.9 % / Num. measured all: 92567 / Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 81.8 % / Rmerge(I) obs: 0.29 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→19.93 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2293632.74 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.9899 Å2 / ksol: 0.272956 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 7.5 % / Rfactor obs: 0.266 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 73.3 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.451 / % reflection Rfree: 7.8 % / Rfactor Rwork: 0.385 |