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- PDB-3my1: Structure of CDK9/cyclinT1 in complex with DRB -

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Basic information

Entry
Database: PDB / ID: 3my1
TitleStructure of CDK9/cyclinT1 in complex with DRB
Components
  • Cell division protein kinase 9
  • Cyclin-T1
KeywordsTRANSCRIPTION/PROTEIN BINDING/INHIBITOR / CDK-cyclin complex / phosphorylated / TRANSCRIPTION-PROTEIN BINDING-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 / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 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 / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / 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 / transcription elongation factor 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 / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / cyclin-dependent kinase / Tat-mediated elongation of the HIV-1 transcript / cyclin-dependent protein serine/threonine kinase activity / 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 / 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 / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / molecular condensate scaffold activity / transcription coactivator binding / PML body / cytoplasmic ribonucleoprotein granule / kinase activity / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / cell population proliferation / protein kinase activity / transcription cis-regulatory region binding / regulation of cell cycle / 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 / 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
PHOSPHATE ION / Chem-RFZ / Cyclin-T1 / Cyclin-dependent kinase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement / Resolution: 2.8 Å
AuthorsBaumli, S. / Johnson, L.N.
CitationJournal: Chem.Biol. / Year: 2010
Title: Halogen bonds form the basis for selective P-TEFb inhibition by DRB
Authors: Baumli, S. / Endicott, J.A. / Johnson, L.N.
History
DepositionMay 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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
Revision 1.3Oct 30, 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: Cell division protein kinase 9
B: Cyclin-T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0489
Polymers68,1742
Non-polymers8757
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-12 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.789, 173.789, 99.221
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 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: 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: 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, 43 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-RFZ / 5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole


Mass: 319.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12Cl2N2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 4.23 Å3/Da / Density % sol: 70.92 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.5
Details: 12% PEG 1000, 100mM sodium/potassium phosphate at pH 6.2, 500mM NaCl, 2mM TCEP as a reservoir solution, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0055 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2008
RadiationMonochromator: Single Silicon (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0055 Å / Relative weight: 1
ReflectionResolution: 2.8→38.49 Å / Num. all: 27750 / Num. obs: 27472 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 84.37 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 6.87
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: Rigid body refinement
Starting model: PDB ENTRY 3BLH

3blh


Resolution: 2.8→38.476 Å / SU ML: 0.41 / σ(F): 1.11 / Phase error: 21.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 2747 5.02 %
Rwork0.1732 --
obs0.1753 27344 99.44 %
all-55018 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.824 Å2 / ksol: 0.305 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.5927 Å20 Å20 Å2
2---9.5927 Å2-0 Å2
3---19.1854 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 55 36 4699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084763
X-RAY DIFFRACTIONf_angle_d1.1586452
X-RAY DIFFRACTIONf_dihedral_angle_d16.8521766
X-RAY DIFFRACTIONf_chiral_restr0.071720
X-RAY DIFFRACTIONf_plane_restr0.005811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.84840.32611290.29332593X-RAY DIFFRACTION99
2.8484-2.90010.27591500.27082587X-RAY DIFFRACTION100
2.9001-2.95590.25791260.24912547X-RAY DIFFRACTION99
2.9559-3.01620.27791450.2272652X-RAY DIFFRACTION99
3.0162-3.08180.24081180.21552664X-RAY DIFFRACTION100
3.0818-3.15340.26611400.20382546X-RAY DIFFRACTION100
3.1534-3.23220.26381590.21062593X-RAY DIFFRACTION100
3.2322-3.31960.28831100.19322640X-RAY DIFFRACTION100
3.3196-3.41720.2311300.19032624X-RAY DIFFRACTION100
3.4172-3.52740.22181350.17532621X-RAY DIFFRACTION100
3.5274-3.65340.23591620.16332585X-RAY DIFFRACTION100
3.6534-3.79960.16141390.16442557X-RAY DIFFRACTION100
3.7996-3.97230.26011240.1632609X-RAY DIFFRACTION100
3.9723-4.18150.18671600.14372591X-RAY DIFFRACTION100
4.1815-4.44320.18961180.13692637X-RAY DIFFRACTION100
4.4432-4.78560.17521440.13652601X-RAY DIFFRACTION100
4.7856-5.26610.19111550.13252607X-RAY DIFFRACTION100
5.2661-6.02570.16531230.14752589X-RAY DIFFRACTION99
6.0257-7.58220.21321490.15142597X-RAY DIFFRACTION99
7.5822-38.480.16611310.14592501X-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)
11.43860.411-0.77681.44660.36740.73950.0270.3235-0.4744-0.15420.0909-0.27260.23220.4755-0.14930.49360.08070.00910.7714-0.07840.552447.8812-11.6093-20.9891
21.8665-0.7991-0.53980.94440.16441.93650.2772-0.1673-0.9310.7661-0.24290.06550.98060.0354-0.11031.056-0.162-0.23750.50460.19750.855148.1316-20.41646.1543
31.9738-0.5654-0.47481.35830.22541.84260.07290.21310.352-0.00390.0437-0.1048-0.14140.0162-0.06430.2952-0.0408-0.07820.458-0.1010.389621.46593.8125-19.9075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 6:108)
2X-RAY DIFFRACTION2chain A and (resseq 109:327)
3X-RAY DIFFRACTION3chain B

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