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Open data
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Basic information
Entry | Database: PDB / ID: 2w99 | ||||||
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Title | Crystal Structure of CDK4 in complex with a D-type cyclin | ||||||
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![]() | CELL CYCLE / SERINE/THREONINE-PROTEIN KINASE / CHROMOSOMAL REARRANGEMENT / ATP-BINDING / TRANSFERASE / POLYMORPHISM / CELL DIVISION / PROTO-ONCOGENE / PHOSPHOPROTEIN / DISEASE MUTATION / NUCLEOTIDE-BINDING / CYCLIN DEPENDENT KINASE / KINASE / CYCLIN / ONCOLOGY / DRUG DESGN | ||||||
Function / homology | ![]() re-entry into mitotic cell cycle / cyclin D3-CDK4 complex / cyclin D1-CDK4 complex / cyclin D2-CDK4 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / cellular response to ionomycin / regulation of transcription initiation by RNA polymerase II / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 ...re-entry into mitotic cell cycle / cyclin D3-CDK4 complex / cyclin D1-CDK4 complex / cyclin D2-CDK4 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / cellular response to ionomycin / regulation of transcription initiation by RNA polymerase II / 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 / regulation of type B pancreatic cell proliferation / RUNX3 regulates WNT signaling / response to leptin / positive regulation of mammary gland epithelial cell proliferation / Transcriptional regulation by RUNX2 / cellular response to phorbol 13-acetate 12-myristate / cyclin-dependent protein serine/threonine kinase activator activity / proline-rich region binding / Regulation of RUNX1 Expression and Activity / cyclin-dependent protein serine/threonine kinase regulator activity / mammary gland epithelial cell proliferation / response to UV-A / negative regulation of epithelial cell differentiation / fat cell differentiation / PTK6 Regulates Cell Cycle / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / RUNX3 regulates p14-ARF / positive regulation of cyclin-dependent protein serine/threonine kinase activity / Transcriptional Regulation by VENTX / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / cyclin-dependent protein kinase holoenzyme complex / bicellular tight junction / mammary gland alveolus development / positive regulation of G1/S transition of mitotic cell cycle / cyclin-dependent kinase / cellular response to interleukin-4 / cyclin-dependent protein serine/threonine kinase activity / endoplasmic reticulum unfolded protein response / mitotic G1 DNA damage checkpoint signaling / regulation of G2/M transition of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / lactation / transcription repressor complex / cyclin binding / : / Ubiquitin-dependent degradation of Cyclin D / liver regeneration / neuron differentiation / Oncogene Induced Senescence / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / Wnt signaling pathway / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / transcription corepressor activity / Cyclin D associated events in G1 / positive regulation of fibroblast proliferation / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / cellular response to lipopolysaccharide / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / transcription regulator complex / regulation of cell cycle / protein kinase activity / response to xenobiotic stimulus / positive regulation of protein phosphorylation / cell division / protein phosphorylation / protein serine kinase activity / centrosome / DNA damage response / positive regulation of cell population proliferation / chromatin / nucleolus / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Day, P.J. / Cleasby, A. / Tickle, I.J. / Reilly, M.O. / Coyle, J.E. / Holding, F.P. / McMenamin, R.L. / Yon, J. / Chopra, R. / Lengauer, C. / Jhoti, H. | ||||||
![]() | ![]() Title: Crystal Structure of Human Cdk4 in Complex with a D-Type Cyclin. Authors: Day, P.J. / Cleasby, A. / Tickle, I.J. / O'Reilly, M. / Coyle, J.E. / Holding, F.P. / Mcmenamin, R.L. / Yon, J. / Chopra, R. / Lengauer, C. / Jhoti, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.6 KB | Display | ![]() |
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PDB format | ![]() | 93.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436 KB | Display | ![]() |
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Full document | ![]() | 469.6 KB | Display | |
Data in XML | ![]() | 26.2 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2w96C ![]() 2w9fC ![]() 2w9zC ![]() 1blxS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 30990.307 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 34544.625 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-44,48-303 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED RESIDUE IN CHAIN B, GLY 43 TO GLU ENGINEERED RESIDUE IN CHAIN B, GLY 44 TO GLU ...ENGINEERED |
Sequence details | RESIDUES 1-271 WERE EXPRESSED, BUT THE N AND C-TERMINAL WERE DISORDERED AND THEREFORE NOT COMPLETE ...RESIDUES 1-271 WERE EXPRESSED, BUT THE N AND C-TERMINAL WERE DISORDERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.28 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 13, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→94.5 Å / Num. obs: 17640 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 78.76 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.8→2.91 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.5 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BLX Resolution: 2.8→94.49 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY WHERE THE DENSITY WAS NOT CLEAR. IN REGIONS WHERE THE DENSITY WAS UNINTERPRETABLE OR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY WHERE THE DENSITY WAS NOT CLEAR. IN REGIONS WHERE THE DENSITY WAS UNINTERPRETABLE OR ABSENT, RESIDUES WERE OMITTED.
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Displacement parameters | Biso mean: 86.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→94.49 Å
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LS refinement shell | Resolution: 2.8→2.97 Å / Total num. of bins used: 9
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