+
Open data
-
Basic information
Entry | Database: PDB / ID: 2w9f | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of CDK4 in complex with a D-type cyclin | ||||||
![]() |
| ||||||
![]() | 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 113.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 87 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 461.2 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2w96C ![]() 2w99C ![]() 2w9zC ![]() 1blxS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 30990.307 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 34620.723 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 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 59.94 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 24, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→60.9 Å / Num. obs: 16778 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 82.07 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.85→3 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.9 / % possible all: 99.3 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BLX Resolution: 2.85→93.66 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES WERE MODELLED STEREOCHEMICALLY WHEN POSSIBLE
| ||||||||||||||||||||
Displacement parameters | Biso mean: 84.35 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→93.66 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.85→3.02 Å / Total num. of bins used: 9
|