+Open data
-Basic information
Entry | Database: PDB / ID: 3lq5 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of CDK9/CyclinT in complex with S-CR8 | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION/INHIBITOR / TRANSCRIPTIONAL CDK-CYCLIN COMPLEX / PHOSPHORYLATED / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / NUCLEUS / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / TRANSCRIPTION REGULATION / TRANSFERASE / CELL CYCLE / CELL DIVISION / HOST-VIRUS INTERACTION / TRANSCRIPTION-INHIBITOR complex | ||||||
Function / homology | Function and homology information P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / nucleus localization / transcription elongation factor activity / cyclin-dependent protein serine/threonine kinase activator activity ...P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / nucleus localization / transcription elongation factor activity / cyclin-dependent protein serine/threonine kinase activator activity / cyclin-dependent kinase / positive regulation of DNA-templated transcription, elongation / positive regulation by host of viral transcription / cyclin-dependent protein serine/threonine kinase activity / RNA polymerase binding / [RNA-polymerase]-subunit kinase / negative regulation of protein localization to chromatin / transcription elongation-coupled chromatin remodeling / regulation of cyclin-dependent protein serine/threonine kinase activity / replication fork processing / cellular response to cytokine stimulus / RNA polymerase II CTD heptapeptide repeat kinase activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / molecular condensate scaffold activity / transcription elongation factor complex / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PML body / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / kinase activity / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription cis-regulatory region binding / cell population proliferation / transcription by RNA polymerase II / regulation of cell cycle / protein kinase activity / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein phosphorylation / cell division / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Rigid Body Refinement / Resolution: 3 Å | ||||||
Authors | Hole, A.J. / Endicott, J.A. / Baumli, S. | ||||||
Citation | Journal: Genes Cancer / Year: 2010 Title: CDK Inhibitors Roscovitine and CR8 Trigger Mcl-1 Down-Regulation and Apoptotic Cell Death in Neuroblastoma Cells Authors: Bettayeb, K. / Baunbak, D. / Delehouze, C. / Loaec, N. / Hole, A.J. / Baumli, S. / Endicott, J.A. / Douc-Rasy, S. / Benard, J. / Oumata, N. / Galons, H. / Meijer, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3lq5.cif.gz | 246.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3lq5.ent.gz | 199.3 KB | Display | PDB format |
PDBx/mmJSON format | 3lq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lq5_validation.pdf.gz | 719.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3lq5_full_validation.pdf.gz | 734.2 KB | Display | |
Data in XML | 3lq5_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 3lq5_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/3lq5 ftp://data.pdbj.org/pub/pdb/validation_reports/lq/3lq5 | HTTPS FTP |
-Related structure data
Related structure data | 3blhS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38054.082 Da / Num. of mol.: 1 / Fragment: Kinase Domain, UNP residues 2-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC2L4, CDK9 / Plasmid: PVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
---|---|
#2: Protein | Mass: 30119.426 Da / Num. of mol.: 1 / Fragment: Cyclin Domain, UNP residues 2-259 / Mutation: Q77R, E96G, F241L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1 / Plasmid: PVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: O60563 |
#3: Chemical | ChemComp-SLQ / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.74 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 14% PEG 1000, 100mM NaK-Phosphate pH 6.2, 500mM NaCl, 4mM TCEP , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3→50.01 Å / Num. all: 22223 / Num. obs: 21867 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 96.7 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 7.44 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3222 / % possible all: 99.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: Rigid Body Refinement Starting model: PDB ENTRY 3BLH Resolution: 3→37.343 Å / FOM work R set: 0.854 / SU ML: 0.37 / σ(F): 1.96 / Phase error: 22.38 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.268 Å2 / ksol: 0.303 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.57 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→37.343 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|