1JOW | pdb_00001jow

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.323 (Depositor), 0.318 (DCC) 
  • R-Value Work: 
    0.266 (Depositor), 0.265 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1JOW

This is version 1.3 of the entry. See complete history

Literature

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

Schulze-Gahmen, U.Kim, S.H.

(2002) Nat Struct Biol 9: 177-181

  • DOI: https://doi.org/10.1038/nsb756
  • Primary Citation 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.


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

Macromolecule Content 

  • Total Structure Weight: 63.73 kDa 
  • Atom Count: 3,986 
  • Modeled Residue Count: 520 
  • Deposited Residue Count: 562 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CYCLIN HOMOLOG254Saimiriine gammaherpesvirus 2Mutation(s): 0 
UniProt
Find proteins for Q01043 (Saimiriine herpesvirus 2 (strain 11))
Explore Q01043 
Go to UniProtKB:  Q01043
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01043
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 6308Homo sapiensMutation(s): 0 
Gene Names: CDK6
EC: 2.7.1 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00534 (Homo sapiens)
Explore Q00534 
Go to UniProtKB:  Q00534
PHAROS:  Q00534
GTEx:  ENSG00000105810 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00534
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.323 (Depositor), 0.318 (DCC) 
  • R-Value Work:  0.266 (Depositor), 0.265 (DCC) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.14α = 90
b = 70.14β = 90
c = 448.77γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references