Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.46 kDa 
• Atom Count: 2337 
• Modelled Residue Count: 254 
• Deposited Residue Count: 258 
• Unique protein chains: 1

2I53

Crystal structure of Cyclin K

• PDB DOI: 10.2210/pdb2I53/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-08-23 Released: 2007-01-02 
• Deposition Author(s): Baek, K., Brown, R.S., Birrane, G., Ladias, J.A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.218 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Crystal Structure of Human Cyclin K, a Positive Regulator of Cyclin-dependent Kinase 9.

Baek, K., Brown, R.S., Birrane, G., Ladias, J.A.

(2007) J Mol Biol 366: 563-573

• PubMed: 17169370 
• DOI: 10.1016/j.jmb.2006.11.057
• Primary Citation of Related Structures:  
  2I53


• PubMed Abstract: 
  

Cyclin K and the closely related cyclins T1, T2a, and T2b interact with cyclin-dependent kinase 9 (CDK9) forming multiple nuclear complexes, referred to collectively as positive transcription elongation factor b (P-TEFb). Through phosphorylation of the C-terminal domain of the RNA polymerase II largest subunit, distinct P-TEFb species regulate the transcriptional elongation of specific genes that play central roles in human physiology and disease development, including cardiac hypertrophy and human immunodeficiency virus-1 pathogenesis. We have determined the crystal structure of human cyclin K (residues 11-267) at 1.5 A resolution, which represents the first atomic structure of a P-TEFb subunit. The cyclin K fold comprises two typical cyclin boxes with two short helices preceding the N-terminal box. A prominent feature of cyclin K is an additional helix (H4a) in the first cyclin box that obstructs the binding pocket for the cell-cycle inhibitor p27(Kip1). Modeling of CDK9 bound to cyclin K provides insights into the structural determinants underlying the formation and regulation of this complex. A homology model of human cyclin T1 generated using the cyclin K structure as a template reveals that the two proteins have similar structures, as expected from their high level of sequence identity. Nevertheless, their CDK9-interacting surfaces display significant structural differences, which could potentially be exploited for the design of cyclin-targeted inhibitors of the CDK9-cyclin K and CDK9-cyclin T1 complexes.

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Organizational Affiliation: 

Molecular Medicine Laboratory and Macromolecular Crystallography Unit, Division of Experimental Medicine, Harvard Institutes of Medicine, Harvard Medical School, Boston, MA 02115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin K	A	258	Homo sapiens	Mutation(s): 0  Gene Names: CCNK, CPR4
UniProt & NIH Common Fund Data Resources
Find proteins for O75909 (Homo sapiens) Explore O75909  Go to UniProtKB:  O75909
PHAROS:  O75909 GTEx:  ENSG00000090061

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A], C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.218 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.766	α = 90
b = 69.186	β = 93.3
c = 50.504	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-08-23 
• Released Date: 2007-01-02 
Deposition Author(s): Baek, K., Brown, R.S., Birrane, G., Ladias, J.A.A.

Revision History  

• Version 1.0: 2007-01-02
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance