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Yorodumi- PDB-4cxa: Crystal structure of the human CDK12-cyclin K complex bound to AMPPNP -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cxa | ||||||
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Title | Crystal structure of the human CDK12-cyclin K complex bound to AMPPNP | ||||||
Components |
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Keywords | TRANSFERASE / KINASE | ||||||
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 / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / 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 / positive regulation of transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / 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. / Nowak, R. / Goubin, S. / Mahajan, R.P. / Kopec, J. / Froese, S. / Tallant, C. / Carpenter, E.P. ...Dixon Clarke, S.E. / Elkins, J.M. / Pike, A.C.W. / Nowak, R. / Goubin, S. / Mahajan, R.P. / Kopec, J. / Froese, S. / Tallant, C. / Carpenter, E.P. / Mackenzie, A. / Faust, B. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cxa.cif.gz | 233 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cxa.ent.gz | 179.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/4cxa ftp://data.pdbj.org/pub/pdb/validation_reports/cx/4cxa | HTTPS FTP |
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-Related structure data
Related structure data | 4un0C 4cjy S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 39719.922 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 715-1052 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NYV4, cyclin-dependent kinase #2: 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 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O75909 #3: Chemical | ChemComp-ANP / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 48.72 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.15M DL-MALIC ACID, 20% PEG3350, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97868 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97868 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→30.53 Å / Num. obs: 22908 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 3.15→3.37 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CJY 4cjy Resolution: 3.15→30.529 Å / SU ML: 0.47 / σ(F): 1.35 / Phase error: 32.91 / Stereochemistry target values: ML
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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→30.529 Å
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Refine LS restraints |
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LS refinement shell |
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