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- PDB-3lq5: Structure of CDK9/CyclinT in complex with S-CR8 -

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Basic information

Entry
Database: PDB / ID: 3lq5
TitleStructure of CDK9/CyclinT in complex with S-CR8
Components
  • Cell division protein kinase 9
  • Cyclin-T1
KeywordsTRANSCRIPTION/INHIBITOR / TRANSCRIPTIONAL CDK-CYCLIN COMPLEX / PHOSPHORYLATED / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / NUCLEUS / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / TRANSCRIPTION REGULATION / TRANSFERASE / CELL CYCLE / CELL DIVISION / HOST-VIRUS INTERACTION / TRANSCRIPTION-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 / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription ...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 / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / positive regulation of DNA-templated transcription, elongation / 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 / 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 / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / regulation of DNA repair / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / transcription elongation factor complex / molecular condensate scaffold activity / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of 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 / cell population proliferation / transcription by RNA polymerase II / transcription cis-regulatory region binding / regulation of cell cycle / protein kinase activity / response to xenobiotic stimulus / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / protein phosphorylation / 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-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma ...: / Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-SLQ / Cyclin-T1 / Cyclin-dependent kinase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid Body Refinement / Resolution: 3 Å
AuthorsHole, A.J. / Endicott, J.A. / Baumli, S.
CitationJournal: Genes Cancer / Year: 2010
Title: CDK Inhibitors Roscovitine and CR8 Trigger Mcl-1 Down-Regulation and Apoptotic Cell Death in Neuroblastoma Cells
Authors: Bettayeb, K. / Baunbak, D. / Delehouze, C. / Loaec, N. / Hole, A.J. / Baumli, S. / Endicott, J.A. / Douc-Rasy, S. / Benard, J. / Oumata, N. / Galons, H. / Meijer, L.
History
DepositionFeb 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references / Refinement description / Structure summary
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein kinase 9
B: Cyclin-T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6053
Polymers68,1742
Non-polymers4321
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-12 kcal/mol
Surface area27700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.249, 173.249, 99.241
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 Cell division protein kinase 9 / Cyclin-dependent kinase 9 / Serine/threonine-protein kinase PITALRE / Cell division cycle 2-like ...Cyclin-dependent kinase 9 / Serine/threonine-protein kinase PITALRE / Cell division cycle 2-like protein kinase 4 / C-2K


Mass: 38054.082 Da / Num. of mol.: 1 / Fragment: Kinase Domain, UNP residues 2-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC2L4, CDK9 / Plasmid: PVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein Cyclin-T1 / Cyclin-T / CycT1


Mass: 30119.426 Da / Num. of mol.: 1 / Fragment: Cyclin Domain, UNP residues 2-259 / Mutation: Q77R, E96G, F241L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1 / Plasmid: PVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: O60563
#3: Chemical ChemComp-SLQ / (2S)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol


Mass: 431.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29N7O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 4.2 Å3/Da / Density % sol: 70.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 14% PEG 1000, 100mM NaK-Phosphate pH 6.2, 500mM NaCl, 4mM TCEP , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→50.01 Å / Num. all: 22223 / Num. obs: 21867 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 96.7 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 7.44
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3222 / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.5_2)model building
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.5_2phasing
RefinementMethod to determine structure: Rigid Body Refinement
Starting model: PDB ENTRY 3BLH

3blh


Resolution: 3→37.343 Å / FOM work R set: 0.854 / SU ML: 0.37 / σ(F): 1.96 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 1095 5.01 %Copied from 3BLH dataset
Rwork0.1623 ---
all0.165 21856 --
obs0.165 21856 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.268 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 97.57 Å2
Baniso -1Baniso -2Baniso -3
1--3.708 Å20 Å20 Å2
2---3.708 Å2-0 Å2
3---7.417 Å2
Refinement stepCycle: LAST / Resolution: 3→37.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4548 0 32 9 4589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094685
X-RAY DIFFRACTIONf_angle_d1.1536350
X-RAY DIFFRACTIONf_dihedral_angle_d19.5081743
X-RAY DIFFRACTIONf_chiral_restr0.072708
X-RAY DIFFRACTIONf_plane_restr0.004799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.13660.33571250.26992615X-RAY DIFFRACTION99
3.1366-3.30180.30131430.23332605X-RAY DIFFRACTION99
3.3018-3.50860.25041220.18672652X-RAY DIFFRACTION99
3.5086-3.77920.20531570.16172564X-RAY DIFFRACTION99
3.7792-4.15910.21081400.13532608X-RAY DIFFRACTION98
4.1591-4.75990.17161300.12172603X-RAY DIFFRACTION98
4.7599-5.99290.16871410.1342578X-RAY DIFFRACTION98
5.9929-37.34610.21831370.16482536X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4861-0.0876-0.450.8282-0.01270.77510.04080.3139-0.3326-0.102-0.0529-0.28130.20490.495-0.02620.40930.09640.03190.6921-0.05310.575347.6549-11.295-20.1867
21.8297-0.6541-0.03321.29560.49672.1440.2761-0.2244-0.63980.6779-0.27970.26050.7780.0769-0.02450.9176-0.1617-0.15110.51660.18970.744747.9325-20.51687.2399
31.9199-0.6328-0.0531.430.60961.98030.06010.12130.29150.00820.087-0.3528-0.09150.1466-0.11810.2492-0.0418-0.07780.4176-0.10070.421.37143.8531-19.7671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 6:108)A6 - 108
2X-RAY DIFFRACTION2chain A and (resseq 109:327)A109 - 327
3X-RAY DIFFRACTION3chain BB9 - 259

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