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- PDB-8i0l: Structure of CDK9/cyclin T1 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 8i0l
TitleStructure of CDK9/cyclin T1 in complex with inhibitor
Components
  • Cyclin-T1
  • Cyclin-dependent kinase 9
KeywordsCELL INVASION/INHIBITOR / CDK9 / inhibitor / complex / CELL INVASION / CELL INVASION-INHIBITOR complex
Function / homology
Function and homology information


P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / nucleus localization / transcription elongation factor activity / cyclin-dependent protein serine/threonine kinase activator activity ...P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / nucleus localization / transcription elongation factor activity / cyclin-dependent protein serine/threonine kinase activator activity / cyclin-dependent kinase / positive regulation of DNA-templated transcription, elongation / positive regulation by host of viral transcription / cyclin-dependent protein serine/threonine kinase activity / RNA polymerase binding / [RNA-polymerase]-subunit kinase / negative regulation of protein localization to chromatin / transcription elongation-coupled chromatin remodeling / regulation of cyclin-dependent protein serine/threonine kinase activity / replication fork processing / cellular response to cytokine stimulus / RNA polymerase II CTD heptapeptide repeat kinase activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / regulation of DNA repair / 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 / molecular condensate scaffold activity / transcription elongation factor complex / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PML body / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / kinase activity / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription cis-regulatory region binding / cell population proliferation / transcription by RNA polymerase II / regulation of cell cycle / protein kinase activity / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein phosphorylation / cell division / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
: / Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / Cyclin/Cyclin-like subunit Ssn8 / : / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily ...: / Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / Cyclin/Cyclin-like subunit Ssn8 / : / 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. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-NJ6 / Cyclin-T1 / Cyclin-dependent kinase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsJiang, C. / Ye, Y. / Huang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of CDK9/cyclin T1 in complex with inhibitor
Authors: Jiang, C. / Ye, Y. / Huang, Y.
History
DepositionJan 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-dependent kinase 9
B: Cyclin-T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6323
Polymers68,2622
Non-polymers3701
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-12 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.150, 172.150, 97.292
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Cyclin-dependent kinase 9 / C-2K / Cell division cycle 2-like protein kinase 4 / Cell division protein kinase 9 / ...C-2K / Cell division cycle 2-like protein kinase 4 / Cell division protein kinase 9 / Serine/threonine-protein kinase PITALRE / Tat-associated kinase complex catalytic subunit


Mass: 38199.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK9, CDC2L4, TAK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein Cyclin-T1 / CycT1 / Cyclin-T


Mass: 30062.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O60563
#3: Chemical ChemComp-NJ6 / 2-[(4-azanylcyclohexyl)amino]-7-cyclopentyl-~{N},~{N}-dimethyl-pyrrolo[2,3-d]pyrimidine-6-carboxamide


Mass: 370.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N6O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.06 Å3/Da / Density % sol: 69.74 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 0.1 M sodium potassium phosphate, pH6.6; 10% PEG1000; 0.5 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.6→22.14 Å / Num. obs: 12388 / % possible obs: 99.19 % / Redundancy: 4.6 % / Biso Wilson estimate: 35.65 Å2 / CC1/2: 0.523 / CC star: 0.828 / Rmerge(I) obs: 0.4944 / Rpim(I) all: 0.2668 / Rrim(I) all: 0.5649 / Net I/σ(I): 3.34
Reflection shellResolution: 3.6→3.728 Å / Rmerge(I) obs: 0.6958 / Num. unique obs: 1251 / CC1/2: 0.065 / Rpim(I) all: 0.3864 / Rrim(I) all: 0.801 / % possible all: 99.44

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Processing

Software
NameVersionClassification
PHENIX1.19-4092-000refinement
SCALAdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→22.14 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 599 4.85 %
Rwork0.2333 --
obs0.2346 12359 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→22.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4550 0 27 0 4577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024683
X-RAY DIFFRACTIONf_angle_d0.4746353
X-RAY DIFFRACTIONf_dihedral_angle_d6.052636
X-RAY DIFFRACTIONf_chiral_restr0.037712
X-RAY DIFFRACTIONf_plane_restr0.004802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.960.34121390.29982952X-RAY DIFFRACTION100
3.96-4.530.29261320.25672938X-RAY DIFFRACTION99
4.53-5.690.21181720.21042926X-RAY DIFFRACTION100
5.69-22.140.20681560.17352944X-RAY DIFFRACTION100

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