2W9F

Crystal Structure of CDK4 in complex with a D-type cyclin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystal Structure of Human Cdk4 in Complex with a D-Type Cyclin.

Day, P.J., Cleasby, A., Tickle, I.J., O'Reilly, M., Coyle, J.E., Holding, F.P., Mcmenamin, R.L., Yon, J., Chopra, R., Lengauer, C., Jhoti, H.

(2009) Proc Natl Acad Sci U S A 106: 4166

  • DOI: 10.1073/pnas.0809645106
  • Primary Citation of Related Structures:  
    2W96, 2W99, 2W9F, 2W9Z

  • PubMed Abstract: 

    • The cyclin D1-cyclin-dependent kinase 4 (CDK4) complex is a key regulator of the transition through the G(1) phase of the cell cycle. Among the cyclin/CDKs, CDK4 and cyclin D1 are the most frequently activated by somatic genetic alterations in multiple tumor types ...

    The cyclin D1-cyclin-dependent kinase 4 (CDK4) complex is a key regulator of the transition through the G(1) phase of the cell cycle. Among the cyclin/CDKs, CDK4 and cyclin D1 are the most frequently activated by somatic genetic alterations in multiple tumor types. Thus, aberrant regulation of the CDK4/cyclin D1 pathway plays an essential role in oncogenesis; hence, CDK4 is a genetically validated therapeutic target. Although X-ray crystallographic structures have been determined for various CDK/cyclin complexes, CDK4/cyclin D1 has remained highly refractory to structure determination. Here, we report the crystal structure of CDK4 in complex with cyclin D1 at a resolution of 2.3 A. Although CDK4 is bound to cyclin D1 and has a phosphorylated T-loop, CDK4 is in an inactive conformation and the conformation of the heterodimer diverges from the previously known CDK/cyclin binary complexes, which suggests a unique mechanism for the process of CDK4 regulation and activation.

    Organizational Affiliation: 

    Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
G1/S-SPECIFIC CYCLIN-D1A271Homo sapiensMutation(s): 0 
Gene Names: CCND1, BCL1, PRAD1
UniProt & NIH Common Fund Data Resources
Find proteins for P24385 (Homo sapiens)
Explore P24385 
Go to UniProtKB:  P24385
PHAROS:  P24385
GTEx:  ENSG00000110092 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24385
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 4B306Homo sapiensMutation(s): 3 
Gene Names: CDK4
EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P11802 (Homo sapiens)
Explore P11802 
Go to UniProtKB:  P11802
PHAROS:  P11802
GTEx:  ENSG00000135446 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11802
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58α = 90
b = 64.277β = 90
c = 187.617γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-24
    Changes: Data collection, Other, Source and taxonomy