3TNI

structure of CDK9/cyclin T F241L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The CDK9 C-helix Exhibits Conformational Plasticity That May Explain the Selectivity of CAN508.

Baumli, S.Hole, A.J.Noble, M.E.Endicott, J.A.

(2012) ACS Chem Biol 7: 811-816

  • DOI: 10.1021/cb2004516
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • CDK9 is the kinase of positive transcription elongation factor b and facilitates the transition of paused RNA polymerase II to processive transcription elongation. CDK9 is a validated target for the treatment of cancer, cardiac hypertrophy, and human ...

    CDK9 is the kinase of positive transcription elongation factor b and facilitates the transition of paused RNA polymerase II to processive transcription elongation. CDK9 is a validated target for the treatment of cancer, cardiac hypertrophy, and human immunodeficiency virus. Here we analyze different CDK9/cyclin T variants to identify a form of the complex amenable to use in inhibitor design. To demonstrate the utility of this system, we have determined the crystal structures of CDK9/cyclin T and CDK2/cyclin A bound to the CDK9-specific inhibitor CAN508. Comparison of the structures reveals CDK9-specific conformational changes and identifies a CDK9-specific hydrophobic pocket, adjacent to the αC-helix. By comparison with a previously published structure of CDK9/cyclin T/human immunodeficiency virus TAT we find that the CDK9 αC-helix has a degree of conformational variability that has the potential to be exploited for inhibitor design.


    Organizational Affiliation

    Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K. sonja.baumli@ncl.ac.uk



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 9A331Homo sapiensMutation(s): 0 
Gene Names: CDC2L4CDK9TAK
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
Find proteins for P50750 (Homo sapiens)
Explore P50750 
Go to UniProtKB:  P50750
NIH Common Fund Data Resources
PHAROS  P50750
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-T1B259Homo sapiensMutation(s): 1 
Gene Names: CCNT1
Find proteins for O60563 (Homo sapiens)
Explore O60563 
Go to UniProtKB:  O60563
NIH Common Fund Data Resources
PHAROS  O60563
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.61α = 90
b = 173.61β = 90
c = 97.47γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data scaling
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Database references