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- PDB-3tnh: CDK9/cyclin T in complex with CAN508 -

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Basic information

Entry
Database: PDB / ID: 3tnh
TitleCDK9/cyclin T in complex with CAN508
Components
  • Cyclin-T1
  • Cyclin-dependent kinase 9
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / cyclin / phosphtransfer / cyclin T / phosphorylated on threonine 186 / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


P-TEFb complex / Interactions of Tat with host cellular proteins / nucleus localization / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / positive regulation of protein localization to chromatin / regulation of mRNA 3'-end processing / transcription elongation factor activity / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity ...P-TEFb complex / Interactions of Tat with host cellular proteins / nucleus localization / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / positive regulation of protein localization to chromatin / regulation of mRNA 3'-end processing / transcription elongation factor activity / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 kinase activity / RNA polymerase II CTD heptapeptide repeat T4 kinase activity / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / RNA polymerase II CTD heptapeptide repeat S7 kinase activity / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription elongation-coupled chromatin remodeling / cellular response to cytokine stimulus / replication fork processing / 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 / cyclin-dependent protein serine/threonine kinase activity / Formation of HIV elongation complex in the absence of HIV Tat / 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 / transcription elongation factor complex / positive regulation of transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / transcription coactivator binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / molecular condensate scaffold activity / PML body / cytoplasmic ribonucleoprotein granule / kinase activity / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / cell population proliferation / regulation of cell cycle / protein kinase activity / transcription cis-regulatory region binding / protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / chromatin binding / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus / membrane / cytosol
Similarity search - Function
: / Cyclin-T2-like, C-terminal 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 ...: / Cyclin-T2-like, C-terminal 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 / : / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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-F18 / Cyclin-T1 / Cyclin-dependent kinase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement / Resolution: 3.202 Å
AuthorsBaumli, S. / Hole, A.J. / Endicott, J.A.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: The CDK9 C-helix Exhibits Conformational Plasticity That May Explain the Selectivity of CAN508.
Authors: Baumli, S. / Hole, A.J. / Noble, M.E. / Endicott, J.A.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 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
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,4123
Polymers68,1942
Non-polymers2181
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-7 kcal/mol
Surface area26100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.300, 173.300, 97.220
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


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 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein Cyclin-T1 / CycT1 / Cyclin-T


Mass: 30139.453 Da / Num. of mol.: 1 / Fragment: cyclin boxes, UNP residues 1-259 / Mutation: F241L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1 / Plasmid: PVL1392 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O60563
#3: Chemical ChemComp-F18 / 4-[(E)-(3,5-DIAMINO-1H-PYRAZOL-4-YL)DIAZENYL]PHENOL / CAN508


Mass: 218.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N6O
Has protein modificationY

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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: 4.12 Å3/Da / Density % sol: 70.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 14% PEG 1K, 100mM Na K phosphate, 600mM NaCl, 4mM TCEP, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2011
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.2→49 Å / Num. all: 17928 / Num. obs: 17892 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3.2-3.293.50.5370.81327199.9
14.32-493.40.01641.2194196.3

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: Rigid body refinement
Starting model: 3BLH

3blh


Resolution: 3.202→38.265 Å / SU ML: 0.76 / σ(F): 1.98 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 895 5 %copied from 3BLH
Rwork0.1767 ---
all0.1791 17927 --
obs0.1791 17884 99.76 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.027 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.0684 Å2-0 Å20 Å2
2---4.0684 Å2-0 Å2
3---8.1367 Å2
Refinement stepCycle: LAST / Resolution: 3.202→38.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 0 16 0 4358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134456
X-RAY DIFFRACTIONf_angle_d1.5266043
X-RAY DIFFRACTIONf_dihedral_angle_d13.2751657
X-RAY DIFFRACTIONf_chiral_restr0.092680
X-RAY DIFFRACTIONf_plane_restr0.008762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2023-3.40280.31791320.25852867X-RAY DIFFRACTION100
3.4028-3.66530.27181620.21192808X-RAY DIFFRACTION100
3.6653-4.03380.22851500.17742839X-RAY DIFFRACTION100
4.0338-4.61660.18521380.13842837X-RAY DIFFRACTION100
4.6166-5.81320.19931620.15372818X-RAY DIFFRACTION100
5.8132-38.26820.23511510.18712820X-RAY DIFFRACTION99
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)
16.97162.43510.94691.83660.28874.03270.04410.2101-0.7133-0.22930.0533-0.51970.49840.6026-0.11770.57160.1744-0.01670.6543-0.06340.665847.6159-11.563-20.0382
23.9529-1.9729-0.98463.38650.30512.3688-0.0656-0.12910.60860.1240.0834-0.0996-0.24310.042-0.01940.4328-0.0647-0.1510.6481-0.04850.597521.48173.3241-20.6793
33.723-1.79591.2735.9653-0.5165.64350.2497-0.3454-0.70761.4168-0.25090.72671.3499-0.01810.00361.0566-0.1894-0.04170.52770.07810.798848.5663-19.29855.861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:105))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 1:259))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 106:330))

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