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- PDB-3blh: Crystal Structure of Human CDK9/cyclinT1 -

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Basic information

Entry
Database: PDB / ID: 3blh
TitleCrystal Structure of Human CDK9/cyclinT1
Components
  • Cell division protein kinase 9
  • Cyclin-T1
KeywordsTRANSCRIPTION / transcriptional CDK-cyclin complex / phosphorylated / Alternative splicing / ATP-binding / Kinase / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / Transcription regulation / Transferase / Acetylation / Cell cycle / Cell division / Coiled coil / Host-virus interaction
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 / positive regulation of DNA-templated transcription, elongation / positive regulation by host of viral transcription / 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 / molecular condensate scaffold activity / transcription elongation factor complex / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / 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 / regulation of cell cycle / transcription cis-regulatory region binding / protein kinase activity / response to xenobiotic stimulus / 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
Cyclin-T1 / Cyclin-dependent kinase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.48 Å
AuthorsBaumli, S. / Lolli, G. / Lowe, E.D. / Johnson, L.N.
CitationJournal: Embo J. / Year: 2008
Title: The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation
Authors: Baumli, S. / Lolli, G. / Lowe, E.D. / Troiani, S. / Rusconi, L. / Bullock, A.N. / Debreczeni, J.E. / Knapp, S. / Johnson, L.N.
History
DepositionDec 11, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)68,2963
Polymers68,1742
Non-polymers1221
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-11 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.920, 172.920, 95.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 / C-2K / Cell division cycle 2- ...Cyclin-dependent kinase 9 / Serine/threonine-protein kinase PITALRE / C-2K / Cell division cycle 2-like protein kinase 4


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: 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
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 4.04 Å3/Da / Density % sol: 69.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, 20% PEG 1000, 0.5M NaCl, 4mM TCEP, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2007
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.48→86.46 Å / Num. obs: 37491 / % possible obs: 99.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.48-2.612.80.4721.61546755340.472100
2.61-2.772.80.32.51460952390.3100
2.77-2.962.80.1664.51370549140.166100
2.96-3.22.80.1027.21272245750.102100
3.2-3.512.80.064101159341830.064100
3.51-3.922.80.05310.91052438120.05399.9
3.92-4.532.70.04912.1918833510.04999.9
4.53-5.552.70.04912.4767128230.04999.4
5.55-7.842.60.04611.9553021440.04698.1
7.84-48.742.60.04414.123509160.04476.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.73 Å
Translation2.5 Å48.73 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.004data extraction
ProDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMZ FOR CHAIN A, PDB ENTRY 2PK2 FOR CHAIN B
Resolution: 2.48→48.726 Å / FOM work R set: 0.859 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ml
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3600 4.98 %RANDOM
Rwork0.179 ---
obs-37490 95.5 %-
Solvent computationBsol: 80.734 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 196.83 Å2 / Biso mean: 74.79 Å2 / Biso min: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.896 Å20 Å20 Å2
2---1.896 Å2-0 Å2
3---3.793 Å2
Refinement stepCycle: LAST / Resolution: 2.48→48.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4454 0 8 139 4601
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.6461
X-RAY DIFFRACTIONf_bond_d0.0051
X-RAY DIFFRACTIONf_chiral_restr0.0471
X-RAY DIFFRACTIONf_dihedral_angle_d10.2931
X-RAY DIFFRACTIONf_plane_restr0.0031
X-RAY DIFFRACTIONf_nbd_refined4.0621
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.48-2.4860.299494X-RAY DIFFRACTION13792
2.486-2.4920.31532X-RAY DIFFRACTION13790
2.492-2.4980.284469X-RAY DIFFRACTION13790
2.498-2.5050.32521X-RAY DIFFRACTION13792
2.505-2.5110.288487X-RAY DIFFRACTION13790
2.511-2.5170.292490X-RAY DIFFRACTION13788
2.517-2.5240.273509X-RAY DIFFRACTION13790
2.524-2.530.282516X-RAY DIFFRACTION13793
2.53-2.5370.274477X-RAY DIFFRACTION13790
2.537-2.5430.271519X-RAY DIFFRACTION13793
2.543-2.550.271487X-RAY DIFFRACTION13792
2.55-2.5570.269581X-RAY DIFFRACTION13794
2.557-2.5640.269462X-RAY DIFFRACTION13792
2.564-2.5710.26539X-RAY DIFFRACTION13793
2.571-2.5780.25523X-RAY DIFFRACTION13792
2.578-2.5850.267507X-RAY DIFFRACTION13792
2.585-2.5920.261447X-RAY DIFFRACTION13792
2.592-2.5990.252538X-RAY DIFFRACTION13794
2.599-2.6060.264513X-RAY DIFFRACTION13792
2.606-2.6140.241531X-RAY DIFFRACTION13793
2.614-2.6210.25504X-RAY DIFFRACTION13792
2.621-2.6290.246518X-RAY DIFFRACTION13793
2.629-2.6370.242534X-RAY DIFFRACTION13791
2.637-2.6440.241450X-RAY DIFFRACTION13792
2.644-2.6520.244500X-RAY DIFFRACTION13792
2.652-2.660.251621X-RAY DIFFRACTION13792
2.66-2.6680.261390X-RAY DIFFRACTION13792
2.668-2.6760.218503X-RAY DIFFRACTION13790
2.676-2.6850.216551X-RAY DIFFRACTION13794
2.685-2.6930.228543X-RAY DIFFRACTION13793
2.693-2.7010.238500X-RAY DIFFRACTION13793
2.701-2.710.236457X-RAY DIFFRACTION13792
2.71-2.7190.23506X-RAY DIFFRACTION13791
2.719-2.7270.237500X-RAY DIFFRACTION13791
2.727-2.7360.211480X-RAY DIFFRACTION13790
2.736-2.7450.221614X-RAY DIFFRACTION13792
2.745-2.7540.229475X-RAY DIFFRACTION13794
2.754-2.7640.235475X-RAY DIFFRACTION13792
2.764-2.7730.197516X-RAY DIFFRACTION13792
2.773-2.7830.217537X-RAY DIFFRACTION13794
2.783-2.7920.191438X-RAY DIFFRACTION13790
2.792-2.8020.228538X-RAY DIFFRACTION13792
2.802-2.8120.213505X-RAY DIFFRACTION13791
2.812-2.8220.202527X-RAY DIFFRACTION13791
2.822-2.8320.178526X-RAY DIFFRACTION13790
2.832-2.8420.204470X-RAY DIFFRACTION13794
2.842-2.8530.188463X-RAY DIFFRACTION13789
2.853-2.8630.204526X-RAY DIFFRACTION13793
2.863-2.8740.202494X-RAY DIFFRACTION13794
2.874-2.8850.211553X-RAY DIFFRACTION13794
2.885-2.8960.219550X-RAY DIFFRACTION13793
2.896-2.9080.174504X-RAY DIFFRACTION13793
2.908-2.9190.183480X-RAY DIFFRACTION13791
2.919-2.9310.192517X-RAY DIFFRACTION13793
2.931-2.9430.188488X-RAY DIFFRACTION13789
2.943-2.9550.168517X-RAY DIFFRACTION13790
2.955-2.9670.2519X-RAY DIFFRACTION13791
2.967-2.980.187470X-RAY DIFFRACTION13794
2.98-2.9920.205587X-RAY DIFFRACTION13792
2.992-3.0050.181450X-RAY DIFFRACTION13790
3.005-3.0180.194477X-RAY DIFFRACTION13795
3.018-3.0320.178512X-RAY DIFFRACTION13790
3.032-3.0450.19531X-RAY DIFFRACTION13793
3.045-3.0590.196517X-RAY DIFFRACTION13793
3.059-3.0730.176508X-RAY DIFFRACTION13791
3.073-3.0870.183576X-RAY DIFFRACTION13791
3.087-3.1020.179410X-RAY DIFFRACTION13791
3.102-3.1170.19568X-RAY DIFFRACTION13793
3.117-3.1320.182446X-RAY DIFFRACTION13790
3.132-3.1480.176499X-RAY DIFFRACTION13792
3.148-3.1630.175526X-RAY DIFFRACTION13794
3.163-3.180.186579X-RAY DIFFRACTION13792
3.18-3.1960.17500X-RAY DIFFRACTION13790
3.196-3.2130.184439X-RAY DIFFRACTION13793
3.213-3.230.189529X-RAY DIFFRACTION13792
3.23-3.2480.178502X-RAY DIFFRACTION13793
3.248-3.2660.169549X-RAY DIFFRACTION13794
3.266-3.2840.158542X-RAY DIFFRACTION13794
3.284-3.3030.173478X-RAY DIFFRACTION13792
3.303-3.3220.191491X-RAY DIFFRACTION13792
3.322-3.3420.177482X-RAY DIFFRACTION13792
3.342-3.3620.172540X-RAY DIFFRACTION13792
3.362-3.3820.185513X-RAY DIFFRACTION13791
3.382-3.4030.186475X-RAY DIFFRACTION13792
3.403-3.4250.171504X-RAY DIFFRACTION13795
3.425-3.4470.19526X-RAY DIFFRACTION13792
3.447-3.470.191534X-RAY DIFFRACTION13793
3.47-3.4930.175540X-RAY DIFFRACTION13791
3.493-3.5180.164457X-RAY DIFFRACTION13789
3.518-3.5420.181515X-RAY DIFFRACTION13790
3.542-3.5680.175482X-RAY DIFFRACTION13791
3.568-3.5940.174542X-RAY DIFFRACTION13794
3.594-3.6210.157521X-RAY DIFFRACTION13793
3.621-3.6490.158432X-RAY DIFFRACTION13792
3.649-3.6780.18568X-RAY DIFFRACTION13792
3.678-3.7070.156489X-RAY DIFFRACTION13790
3.707-3.7380.172509X-RAY DIFFRACTION13792
3.738-3.770.164511X-RAY DIFFRACTION13794
3.77-3.8020.157499X-RAY DIFFRACTION13792
3.802-3.8360.156518X-RAY DIFFRACTION13794
3.836-3.8720.165496X-RAY DIFFRACTION13789
3.872-3.9080.151496X-RAY DIFFRACTION13791
3.908-3.9460.143558X-RAY DIFFRACTION13794
3.946-3.9850.163438X-RAY DIFFRACTION13789
3.985-4.0260.137545X-RAY DIFFRACTION13791
4.026-4.0690.144470X-RAY DIFFRACTION13791
4.069-4.1140.132524X-RAY DIFFRACTION13791
4.114-4.1610.124544X-RAY DIFFRACTION13794
4.161-4.2090.127486X-RAY DIFFRACTION13792
4.209-4.2610.131482X-RAY DIFFRACTION13793
4.261-4.3150.128530X-RAY DIFFRACTION13790
4.315-4.3720.115525X-RAY DIFFRACTION13791
4.372-4.4310.121447X-RAY DIFFRACTION13790
4.431-4.4950.117532X-RAY DIFFRACTION13790
4.495-4.5620.124519X-RAY DIFFRACTION13792
4.562-4.6330.109470X-RAY DIFFRACTION13789
4.633-4.7090.13490X-RAY DIFFRACTION13789
4.709-4.790.119513X-RAY DIFFRACTION13792
4.79-4.8770.124482X-RAY DIFFRACTION13791
4.877-4.9710.123514X-RAY DIFFRACTION13789
4.971-5.0720.132515X-RAY DIFFRACTION13791
5.072-5.1820.133475X-RAY DIFFRACTION13790
5.182-5.3020.137517X-RAY DIFFRACTION13793
5.302-5.4350.15506X-RAY DIFFRACTION13792
5.435-5.5820.159511X-RAY DIFFRACTION13790
5.582-5.7460.157466X-RAY DIFFRACTION13791
5.746-5.9310.159511X-RAY DIFFRACTION13787
5.931-6.1420.176483X-RAY DIFFRACTION13787
6.142-6.3880.163464X-RAY DIFFRACTION13788
6.388-6.6780.172450X-RAY DIFFRACTION13779
6.678-7.0290.173449X-RAY DIFFRACTION13781
7.029-7.4680.154523X-RAY DIFFRACTION13794
7.468-8.0420.151491X-RAY DIFFRACTION13791
8.042-8.8470.158469X-RAY DIFFRACTION13785
8.847-10.1170.159408X-RAY DIFFRACTION13774
10.117-12.7090.187325X-RAY DIFFRACTION13759
12.709-48.7360.291281X-RAY DIFFRACTION13750
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.31150.14960.2241.50770.13542.86660.25240.0581-0.58220.3049-0.0961-0.25740.64740.124-0.15150.3749-0.0163-0.12390.21080.06010.592946.9601-17.2911-0.505
22.5213-0.5501-0.33211.32740.281.03650.05680.08010.19970.01960.0315-0.3054-0.04590.042-0.09150.2758-0.0089-0.00760.363-0.04080.313721.78093.3575-20.2161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA8 - 325
2X-RAY DIFFRACTION2chain BB5 - 259

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