4EC9 | pdb_00004ec9

Crystal structure of full-length cdk9 in complex with cyclin t

• PDB DOI: https://doi.org/10.2210/pdb4EC9/pdb

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


• Deposited: 2012-03-26 Released: 2012-09-12 
• Deposition Author(s): Baumli, S., Hole, A.J., Endicott, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

The CDK9 tail determines the reaction pathway of positive transcription elongation factor b.

Baumli, S., Hole, A.J., Wang, L.Z., Noble, M.E., Endicott, J.A.

(2012) Structure 20: 1788-1795

• PubMed: 22959624 
• DOI: https://doi.org/10.1016/j.str.2012.08.011
• Primary Citation of Related Structures:  
  4EC8, 4EC9


• PubMed Abstract: 
  

  CDK9, the kinase of positive transcription elongation factor b (P-TEFb), stimulates transcription elongation by phosphorylating RNA polymerase II and transcription elongation factors. Using kinetic analysis of a human P-TEFb complex consisting of CDK9 and cyclin T, we show that the CDK9 C-terminal tail sequence is important for the catalytic mechanism and imposes an ordered binding of substrates and release of products. Crystallographic analysis of a CDK9/cyclin T complex in which the C-terminal tail partially blocks the ATP binding site reveals a possible reaction intermediate. Biochemical characterization of CDK9 mutants supports a model in which the CDK9 tail cycles through different conformational states. We propose that this mechanism is critical for the pattern of CTD Ser2 phosphorylation on actively transcribed genes.

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Organizational Affiliation: 
• Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK. [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: 73.06 kDa 
• Atom Count: 4,534 
• Modeled Residue Count: 558 
• Deposited Residue Count: 633 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 9	A	373	Homo sapiens	Mutation(s): 0  Gene Names: CDC2L4, CDK9, TAK 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	260	Homo sapiens	Mutation(s): 3  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: 3.21 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.229	α = 90
b = 174.229	β = 90
c = 97.99	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Baumli, S., Hole, A.J., Endicott, J.A.

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary