3TNI

structure of CDK9/cyclin T F241L

• PDB DOI: https://doi.org/10.2210/pdb3TNI/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2011-09-01 Released: 2012-02-15 
• Deposition Author(s): Baumli, S., Hole, A.J., Endicott, J.A.

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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 

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

• PubMed: 22292676 
• DOI: https://doi.org/10.1021/cb2004516
• Primary Citation of Related Structures:  
  3TN8, 3TNH, 3TNI, 3TNW


• 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 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.

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Organizational Affiliation: 

Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.19 kDa 
• Atom Count: 4,489 
• Modelled Residue Count: 550 
• Deposited Residue Count: 590 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 9	A	331	Homo sapiens	Mutation(s): 0  Gene Names: CDC2L4, CDK9 EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P50750 (Homo sapiens) Explore P50750  Go to UniProtKB:  P50750
PHAROS:  P50750 GTEx:  ENSG00000136807

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-T1	B	259	Homo sapiens	Mutation(s): 1  Gene Names: CCNT1
UniProt & NIH Common Fund Data Resources
Find proteins for O60563 (Homo sapiens) Explore O60563  Go to UniProtKB:  O60563
PHAROS:  O60563 GTEx:  ENSG00000129315

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

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 = 173.61	α = 90
b = 173.61	β = 90
c = 97.47	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data scaling
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Baumli, S., Hole, A.J., Endicott, J.A.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2012-05-30
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary