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- PDB-7jv7: Crystal Structure of the yeast RNA Pol II CTD kinase CTDK-1 complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jv7 | ||||||
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Title | Crystal Structure of the yeast RNA Pol II CTD kinase CTDK-1 complex | ||||||
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![]() | TRANSCRIPTION / TRANSFERASE / CDK / kinase | ||||||
Function / homology | ![]() CTDK-1 complex / : / RNA Polymerase II Transcription Elongation / : / cyclin/CDK positive transcription elongation factor complex / positive regulation of translational fidelity / mRNA 3'-end processing / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase ...CTDK-1 complex / : / RNA Polymerase II Transcription Elongation / : / cyclin/CDK positive transcription elongation factor complex / positive regulation of translational fidelity / mRNA 3'-end processing / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / positive regulation of transcription by RNA polymerase I / Estrogen-dependent gene expression / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / Neutrophil degranulation / cyclin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / transcription elongation by RNA polymerase II / translational initiation / positive regulation of transcription elongation by RNA polymerase II / mRNA processing / peptidyl-serine phosphorylation / protein kinase activity / protein phosphorylation / DNA damage response / regulation of transcription by RNA polymerase II / nucleolus / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xie, Y. / Ren, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and activation mechanism of the yeast RNA Pol II CTD kinase CTDK-1 complex. Authors: Xie, Y. / Lord, C.L. / Clarke, B.P. / Ivey, A.L. / Hill, P.S. / McDonald, W.H. / Wente, S.R. / Ren, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 254.9 KB | Display | ![]() |
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PDB format | ![]() | 161.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40667.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CTK1, YKL139W / Production host: ![]() References: UniProt: Q03957, [RNA-polymerase]-subunit kinase |
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#2: Protein | Mass: 38096.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CTK2, YJL006C, J1390 / Production host: ![]() |
#3: Protein | Mass: 34856.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CTK3, YML112W, YM8339.07 / Production host: ![]() |
#4: Chemical | ChemComp-FLC / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: 0.1 M Sodium Citrate pH 5.3, 0.3 M Lithium Chloride, and 17.5% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.004 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 91889 / % possible obs: 89.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 25.9686050695 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.85→1.88 Å / Rmerge(I) obs: 0.53 / Num. unique obs: 4321 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.1018082669 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85055301184→29.2418987215 Å
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Refine LS restraints |
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LS refinement shell |
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