Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 68.30 kDa 
• Atom Count: 4601 
• Residue Count: 547 
• Unique protein chains: 2

3BLH

Crystal Structure of Human CDK9/cyclinT1

• DOI: 10.2210/pdb3BLH/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2007-12-11 Released: 2008-07-01 
• Deposition Author(s): Baumli, S., Lolli, G., Lowe, E.D., Johnson, L.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.221 
• R-Value Work: 0.179 

Literature

The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation

Baumli, S., Lolli, G., Lowe, E.D., Troiani, S., Rusconi, L., Bullock, A.N., Debreczeni, J.E., Knapp, S., Johnson, L.N.

(2008) EMBO J 27: 1907-1918

• PubMed: 18566585 
• DOI: 10.1038/emboj.2008.121
• Primary Citation of Related Structures:  
  3BLQ, 3BLR, 3BLH, 2IVX


• PubMed Abstract: 
  

The positive transcription elongation factor b (P-TEFb) (CDK9/cyclin T (CycT)) promotes mRNA transcriptional elongation through phosphorylation of elongation repressors and RNA polymerase II. To understand the regulation of a transcriptional CDK by its cognate cyclin, we have determined the structures of the CDK9/CycT1 and free cyclin T2. There are distinct differences between CDK9/CycT1 and the cell cycle CDK CDK2/CycA manifested by a relative rotation of 26 degrees of CycT1 with respect to the CDK, showing for the first time plasticity in CDK cyclin interactions. The CDK9/CycT1 interface is relatively sparse but retains some core CDK-cyclin interactions. The CycT1 C-terminal helix shows flexibility that may be important for the interaction of this region with HIV TAT and HEXIM. Flavopiridol, an anticancer drug in phase II clinical trials, binds to the ATP site of CDK9 inducing unanticipated structural changes that bury the inhibitor. CDK9 activity and recognition of regulatory proteins are governed by autophosphorylation. We show that CDK9/CycT1 autophosphorylates on Thr186 in the activation segment and three C-terminal phosphorylation sites. Autophosphorylation on all sites occurs in cis.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 9	A	331	Homo sapiens	Mutation(s): 0  Gene Names: CDK9, CDC2L4, TAK 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 GTEx:  ENSG00000136807

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-T1	B	260	Homo sapiens	Mutation(s): 3  Gene Names: CCNT1
Find proteins for O60563 (Homo sapiens) Explore O60563  Go to UniProtKB:  O60563
NIH Common Fund Data Resources
PHAROS:  O60563 GTEx:  ENSG00000129315

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

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: 2.48 Å
• R-Value Free: 0.221 
• R-Value Work: 0.179 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.92	α = 90
b = 172.92	β = 90
c = 95.76	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ProDC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-12-11 
• Released Date: 2008-07-01 
Deposition Author(s): Baumli, S., Lolli, G., Lowe, E.D., Johnson, L.N.

Revision History 

• Version 1.0: 2008-07-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance