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- PDB-7jv7: Crystal Structure of the yeast RNA Pol II CTD kinase CTDK-1 complex -

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Basic information

Entry
Database: PDB / ID: 7jv7
TitleCrystal Structure of the yeast RNA Pol II CTD kinase CTDK-1 complex
Components
  • CTD kinase subunit alpha
  • CTD kinase subunit beta
  • CTD kinase subunit gamma
KeywordsTRANSCRIPTION / TRANSFERASE / CDK / kinase
Function / homology
Function and homology information


carboxy-terminal domain protein kinase complex / CTDK-1 complex / cyclin/CDK positive transcription elongation factor complex / cyclin-dependent protein serine/threonine kinase activator activity / mRNA 3'-end processing / positive regulation of translational fidelity / 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 ...carboxy-terminal domain protein kinase complex / CTDK-1 complex / cyclin/CDK positive transcription elongation factor complex / cyclin-dependent protein serine/threonine kinase activator activity / mRNA 3'-end processing / positive regulation of translational fidelity / 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 / Neutrophil degranulation / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / translational initiation / protein kinase activity / DNA damage response / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CTD kinase subunit gamma Ctk3, C-terminal / CTD kinase subunit gamma / CTD kinase subunit gamma CTK3 C-terminus / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma ...CTD kinase subunit gamma Ctk3, C-terminal / CTD kinase subunit gamma / CTD kinase subunit gamma CTK3 C-terminus / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRATE ANION / CTD kinase subunit beta / CTD kinase subunit gamma / CTD kinase subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85055301184 Å
AuthorsXie, Y. / Ren, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM133743 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
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
DepositionAug 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTD kinase subunit alpha
B: CTD kinase subunit beta
C: CTD kinase subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8104
Polymers113,6213
Non-polymers1891
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-56 kcal/mol
Surface area37840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.170, 71.091, 84.797
Angle α, β, γ (deg.)79.076, 86.220, 72.686
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein CTD kinase subunit alpha / CTDK-I subunit alpha / CTD kinase 58 kDa subunit / CTD kinase subunit 1


Mass: 40667.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CTK1, YKL139W / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q03957, [RNA-polymerase]-subunit kinase
#2: Protein CTD kinase subunit beta / CTDK-I subunit beta / CTD kinase 38 kDa subunit / CTD kinase subunit 2


Mass: 38096.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CTK2, YJL006C, J1390 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P46962
#3: Protein CTD kinase subunit gamma / CTDK-I gamma subunit / CTD kinase 32 kDa subunit / CTD kinase subunit 3


Mass: 34856.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CTK3, YML112W, YM8339.07 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P46963
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.004 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.53 / Num. unique obs: 4321

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85055301184→29.2418987215 Å / SU ML: 0.245922209401 / Cross valid method: FREE R-VALUE / σ(F): 1.96186904856 / Phase error: 21.7262698007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221728843375 1999 2.17592441411 %
Rwork0.183545427637 89870 -
obs0.184364153002 91869 89.1975338609 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.1018082669 Å2
Refinement stepCycle: LAST / Resolution: 1.85055301184→29.2418987215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7140 0 13 549 7702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007377699676247431
X-RAY DIFFRACTIONf_angle_d0.86521669269310080
X-RAY DIFFRACTIONf_chiral_restr0.05140793009991143
X-RAY DIFFRACTIONf_plane_restr0.005436799551551275
X-RAY DIFFRACTIONf_dihedral_angle_d7.275598379646334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8506-1.89680.3446329648731350.2832249767786031X-RAY DIFFRACTION83.3243243243
1.8968-1.94810.3102599085661430.2486184034546451X-RAY DIFFRACTION90.2916609612
1.9481-2.00540.2577712796371460.2233844492026591X-RAY DIFFRACTION91.3491525424
2.0054-2.07010.2441288153131460.208494156766553X-RAY DIFFRACTION91.3292433538
2.0701-2.14410.2525243938981450.2039105401616523X-RAY DIFFRACTION90.7581325711
2.1441-2.22990.2501472318061450.2024178633126518X-RAY DIFFRACTION90.2234258632
2.2299-2.33140.2571729085151430.19583251666401X-RAY DIFFRACTION89.3500819224
2.3314-2.45420.2420199138171390.1986508391386264X-RAY DIFFRACTION86.8556701031
2.4542-2.60790.2220920254591230.1913640382175535X-RAY DIFFRACTION76.7082429501
2.6079-2.80910.2201637900941500.1880738881736722X-RAY DIFFRACTION93.5220468155
2.8091-3.09150.2250888843081510.1900133138166769X-RAY DIFFRACTION93.9069073144
3.0915-3.53820.2156513826291480.1751576289216678X-RAY DIFFRACTION92.9466230937
3.5382-4.45520.1900758656661430.1491215055986417X-RAY DIFFRACTION89.0457445364
4.4552-29.240.1874017223211420.1653612587856417X-RAY DIFFRACTION89.2745338233

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