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- PDB-3tn8: CDK9/cyclin T in complex with CAN508 -

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Basic information

Entry
Database: PDB / ID: 3tn8
TitleCDK9/cyclin T in complex with CAN508
Components
  • Cyclin-T1
  • Cyclin-dependent kinase 9
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / cyclin dependent kinase / Kinase / cyclin / phosphotransfer / CDK-cyclin complex / 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 mRNA 3'-end processing / positive regulation of protein localization to chromatin / regulation of muscle cell differentiation / transcription elongation factor activity / regulation of cyclin-dependent protein serine/threonine 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 mRNA 3'-end processing / positive regulation of protein localization to chromatin / regulation of muscle cell differentiation / transcription elongation factor activity / regulation of cyclin-dependent protein serine/threonine kinase activity / host-mediated activation of viral transcription / cyclin-dependent protein serine/threonine kinase activator activity / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase / negative regulation of protein localization to chromatin / 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 / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / regulation of DNA repair / Formation of HIV elongation complex in the absence of HIV Tat / 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 / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / molecular condensate scaffold activity / PML body / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / kinase activity / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / cell population proliferation / protein phosphorylation / protein kinase activity / transcription cis-regulatory region binding / regulation of cell cycle / 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 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-F18 / PHOSPHATE ION / Cyclin-T1 / Cyclin-dependent kinase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 2.95 Å
AuthorsBaumli, S. / Hole, A.J. / Endicott, J.E.
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 1.1Jun 13, 2012Group: Database references
Revision 1.2Sep 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 1.3Nov 6, 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)68,8618
Polymers68,1742
Non-polymers6876
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-22 kcal/mol
Surface area27830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.420, 173.420, 97.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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Protein , 2 types, 2 molecules AB

#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: 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 / CycT1 / Cyclin-T


Mass: 30119.426 Da / Num. of mol.: 1 / Fragment: 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

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Non-polymers , 4 types, 14 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.16 Å3/Da / Density % sol: 70.4 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 12% PEG 1K, 50 mM sodium/potassium phosphate, 4 mM TCEP, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 14, 2009
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.95→43.355 Å / Num. all: 23081 / Num. obs: 23081 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.95-3.113.70.5891.21255733940.589100
3.11-3.33.70.3182.41185231960.318100
3.3-3.533.70.1724.21115730060.172100
3.53-3.813.70.1116.51023127720.111100
3.81-4.173.70.0749951925840.074100
4.17-4.663.70.05910.8850523170.059100
4.66-5.393.60.0639.9743920570.063100
5.39-6.63.50.0856.9613817400.08599.8
6.6-9.333.40.04214449113040.04298.3
9.33-81.9233.70.0321.126537110.0396.4

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
PHENIXphasing
RefinementMethod to determine structure: rigid body refinement
Starting model: 3BLH

3blh


Resolution: 2.95→37.068 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8502 / SU ML: 0.77 / σ(F): 2 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 1161 5.03 %copied from 3BLH
Rwork0.1763 ---
obs0.1786 23077 99.81 %-
all-23121 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.643 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 214.67 Å2 / Biso mean: 95.0724 Å2 / Biso min: 45.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.6357 Å20 Å20 Å2
2---0.6357 Å2-0 Å2
3---1.2714 Å2
Refinement stepCycle: LAST / Resolution: 2.95→37.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 43 8 4587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054678
X-RAY DIFFRACTIONf_angle_d0.8426343
X-RAY DIFFRACTIONf_chiral_restr0.055707
X-RAY DIFFRACTIONf_plane_restr0.003799
X-RAY DIFFRACTIONf_dihedral_angle_d13.6521745
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.08420.3581400.314127542894100
3.0842-3.24680.31791560.253927292885100
3.2468-3.450.26751240.216927682892100
3.45-3.71620.26111600.199227332893100
3.7162-4.08970.20861470.16827472894100
4.0897-4.68050.17771360.139627402876100
4.6805-5.89320.19941520.154927402892100
5.8932-37.07140.20361460.1652705285198
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)
12.59070.3860.11340.90950.36931.48970.06440.2563-0.4534-0.1373-0.03920.05190.39480.3606-0.06580.54910.0832-0.03330.7747-0.01720.717347.3265-11.3935-21.0041
22.298-0.86130.63442.5647-0.09142.70770.2716-0.1046-0.49810.7135-0.22580.40180.73030.0425-0.04320.9223-0.1457-0.05790.66560.06880.826148.0936-20.33425.631
33.2692-0.6763-0.23241.90.32241.9790.0438-0.14390.28370.12150.008-0.2126-0.15270.0314-0.02270.346-0.0343-0.10850.4677-0.02560.344321.35843.958-20.9055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:105)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 106:330)A0
3X-RAY DIFFRACTION3chain 'B' and (resseq 1:259)B0

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