+Open data
-Basic information
Entry | Database: PDB / ID: 4un0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the human CDK12-cyclinK complex | |||||||||
Components |
| |||||||||
Keywords | TRANSFERASE | |||||||||
Function / homology | Function and homology information cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / negative regulation of stem cell differentiation / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase ...cyclin K-CDK12 complex / cyclin K-CDK13 complex / nuclear cyclin-dependent protein kinase holoenzyme complex / regulation of MAP kinase activity / cyclin/CDK positive transcription elongation factor complex / negative regulation by host of viral genome replication / negative regulation of stem cell differentiation / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase / regulation of cyclin-dependent protein serine/threonine kinase activity / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / regulation of signal transduction / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / cyclin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / RNA splicing / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / mRNA processing / transcription by RNA polymerase II / protein autophosphorylation / protein kinase activity / nuclear speck / cell cycle / cell division / protein serine kinase activity / DNA damage response / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | |||||||||
Authors | Dixon Clarke, S.E. / Elkins, J.M. / Pike, A.C.W. / Chaikuad, A. / Goubin, S. / Krojer, T. / Sorrell, F.J. / Nowak, R. / Williams, E. / Kopec, J. ...Dixon Clarke, S.E. / Elkins, J.M. / Pike, A.C.W. / Chaikuad, A. / Goubin, S. / Krojer, T. / Sorrell, F.J. / Nowak, R. / Williams, E. / Kopec, J. / Mahajan, R.P. / Burgess-Brown, N. / Carpenter, E.P. / Knapp, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. | |||||||||
Citation | Journal: Sci.Rep. / Year: 2015 Title: Structures of the Cdk12/Cyck Complex with AMP-Pnp Reveal a Flexible C-Terminal Kinase Extension Important for ATP Binding. Authors: Dixon-Clarke, S.E. / Elkins, J.M. / Cheng, S.G. / Morin, G.B. / Bullock, A.N. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4un0.cif.gz | 216.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4un0.ent.gz | 170.2 KB | Display | PDB format |
PDBx/mmJSON format | 4un0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/4un0 ftp://data.pdbj.org/pub/pdb/validation_reports/un/4un0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4cxaC 2i53S 4bcgS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 30443.148 Da / Num. of mol.: 2 / Fragment: CYCLIN K, RESIDUES 11-267 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O75909 #2: Protein | Mass: 37819.672 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 715-1038 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NYV4, cyclin-dependent kinase |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: 20% PEG3350, 10% ETGLY, 0.1M BISTRIS PROPANE PH6.5, 0.2M SODIUM NITRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→57.82 Å / Num. obs: 22936 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 61.62 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.15→3.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2 / % possible all: 99.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2I53 AND 4BCG Resolution: 3.15→57.821 Å / SU ML: 0.43 / σ(F): 1.36 / Phase error: 27.52 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→57.821 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|