Biological Assembly 1  

 3D View: Structure | Electron Density

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: 63.73 kDa 
• Atom Count: 3986 
• Residue Count: 520 
• Unique protein chains: 2

1JOW

Crystal structure of a complex of human CDK6 and a viral cyclin

• DOI: 10.2210/pdb1JOW/pdb

• Classification: CELL CYCLE/TRANSFERASE
• Organism(s): Saimiriine gammaherpesvirus 2, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2001-07-31 Released: 2002-02-27 
• Deposition Author(s): Schulze-Gahmen, U., Kim, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.323 
• R-Value Work: 0.266 

Literature

Structural basis for CDK6 activation by a virus-encoded cyclin.

Schulze-Gahmen, U., Kim, S.H.

(2002) Nat Struct Biol 9: 177-181

• PubMed: 11828325 
• DOI: 10.1038/nsb756
• Primary Citation of Related Structures:  
  1JOW


• PubMed Abstract: 
  

Cyclin from herpesvirus saimiri (Vcyclin) preferentially forms complexes with cyclin-dependent kinase 6 (CDK6) from primate host cells. These complexes show higher kinase activity than host cell CDKs in complex with cellular cyclins and are resistant to cyclin-dependent inhibitory proteins (CDKIs). The crystal structure of human CDK6--Vcyclin in an active state was determined to 3.1 A resolution to better understand the structural basis of CDK6 activation by viral cyclins. The unphosphorylated CDK6 in complex with Vcyclin has many features characteristic of cyclinA-activated, phosphorylated CDK2. There are, however, differences in the conformation at the tip of the T-loop and its interactions with Vcyclin. Residues in the N-terminal extension of Vcyclin wrap around the tip of the CDK6 T-loop and form a short beta-sheet with the T-loop backbone. These interactions lead to a 20% larger buried surface in the CDK6--Vcyclin interface than in the CDK2--cyclinA complex and are probably largely responsible for the specificity of Vcyclin for CDK6 and resistance of the complex to inhibition by INK-type CDKIs.

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Related Citations: 

• Crystallization of a Complex between Human CDK6 and a Virus-encoded Cyclin is Critically Dependent on the Addition of Small Charged Organic Molecules
  Schulze-Gahmen, U., Kim, S.H.
  () To be published --: --

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Organizational Affiliation: 

Physical Bioscience Division at E. O. Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN HOMOLOG	A	254	Saimiriine gammaherpesvirus 2	Mutation(s): 0
Find proteins for Q01043 (Saimiriine herpesvirus 2 (strain 11)) Explore Q01043  Go to UniProtKB:  Q01043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN KINASE 6	B	308	Homo sapiens	Mutation(s): 0  Gene Names: CDK6, CDKN6 EC: 2.7.1 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for Q00534 (Homo sapiens) Explore Q00534  Go to UniProtKB:  Q00534
NIH Common Fund Data Resources
PHAROS:  Q00534 GTEx:  ENSG00000105810

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.323 
• R-Value Work: 0.266 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.14	α = 90
b = 70.14	β = 90
c = 448.77	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-07-31 
• Released Date: 2002-02-27 
Deposition Author(s): Schulze-Gahmen, U., Kim, S.H.

Revision History 

• Version 1.0: 2002-02-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance