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Yorodumi- PDB-4nst: Crystal structure of human Cdk12/Cyclin K in complex with ADP-alu... -
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-Basic information
Entry | Database: PDB / ID: 4nst | ||||||
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Title | Crystal structure of human Cdk12/Cyclin K in complex with ADP-aluminum fluoride | ||||||
Components |
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Keywords | TRANSFERASE/TRANSCRIPTION / transcription / RNA polymerase II / phosphorylation / TRANSFERASE-TRANSCRIPTION complex | ||||||
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 / cyclin-dependent kinase / positive regulation of DNA-templated transcription, elongation ...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 / cyclin-dependent kinase / positive regulation of DNA-templated transcription, elongation / cyclin-dependent protein serine/threonine kinase activity / [RNA-polymerase]-subunit kinase / regulation of cyclin-dependent protein serine/threonine kinase activity / RNA polymerase II CTD heptapeptide repeat kinase activity / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / cyclin binding / regulation of signal transduction / Formation of HIV elongation complex in the absence of HIV Tat / 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 / RNA splicing / TP53 Regulates Transcription of DNA Repair Genes / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / mRNA processing / protein autophosphorylation / transcription by RNA polymerase II / protein kinase activity / nuclear speck / 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: 2.2 Å | ||||||
Authors | Boesken, C.A. / Farnung, L. / Anand, K. / Geyer, M. | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: The structure and substrate specificity of human Cdk12/Cyclin K. Authors: Bosken, C.A. / Farnung, L. / Hintermair, C. / Merzel Schachter, M. / Vogel-Bachmayr, K. / Blazek, D. / Anand, K. / Fisher, R.P. / Eick, D. / Geyer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nst.cif.gz | 484.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nst.ent.gz | 390.2 KB | Display | PDB format |
PDBx/mmJSON format | 4nst.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nst_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4nst_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4nst_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 4nst_validation.cif.gz | 67.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/4nst ftp://data.pdbj.org/pub/pdb/validation_reports/ns/4nst | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 40764.992 Da / Num. of mol.: 2 / Fragment: Protein kinase domain, residues 714-1063 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK12, CRK7, CRKRS, KIAA0904 / Plasmid: pACEBac1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 References: UniProt: Q9NYV4, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase #2: Protein | Mass: 31429.172 Da / Num. of mol.: 2 / Fragment: UNP residues 1-267 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNK, CPR4 / Plasmid: pIDK / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 / References: UniProt: O75909 |
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-Non-polymers , 5 types, 408 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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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: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris, pH 6.5, 20.5% PEG 3350, 0.4 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9785 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2012 |
Radiation | Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.7 Å / Num. all: 65263 / Num. obs: 65263 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.52 Å2 |
Reflection shell | Resolution: 2.2→2.25 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BLQ, 2I53 Resolution: 2.2→48.711 Å / SU ML: 0.38 / σ(F): 2 / Phase error: 26.57 / 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 / Bsol: 42.684 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→48.711 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -10.2535 Å / Origin y: -26.3036 Å / Origin z: -2.7411 Å
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Refinement TLS group | Selection details: all |