6P8G

Crystal structure of CDK4 in complex with CyclinD1 and P27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


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Literature

p27 allosterically activates cyclin-dependent kinase 4 and antagonizes palbociclib inhibition.

Guiley, K.Z.Stevenson, J.W.Lou, K.Barkovich, K.J.Kumarasamy, V.Wijeratne, T.U.Bunch, K.L.Tripathi, S.Knudsen, E.S.Witkiewicz, A.K.Shokat, K.M.Rubin, S.M.

(2019) Science 366

  • DOI: 10.1126/science.aaw2106
  • Primary Citation of Related Structures:  
    6P8G, 6P8F, 6P8H, 6P8E

  • PubMed Abstract: 
  • The p27 protein is a canonical negative regulator of cell proliferation and acts primarily by inhibiting cyclin-dependent kinases (CDKs). Under some circumstances, p27 is associated with active CDK4, but no mechanism for activation has been described. We found that p27, when phosphorylated by tyrosine kinases, allosterically activated CDK4 in complex with cyclin D1 (CDK4-CycD1) ...

    The p27 protein is a canonical negative regulator of cell proliferation and acts primarily by inhibiting cyclin-dependent kinases (CDKs). Under some circumstances, p27 is associated with active CDK4, but no mechanism for activation has been described. We found that p27, when phosphorylated by tyrosine kinases, allosterically activated CDK4 in complex with cyclin D1 (CDK4-CycD1). Structural and biochemical data revealed that binding of phosphorylated p27 (phosp27) to CDK4 altered the kinase adenosine triphosphate site to promote phosphorylation of the retinoblastoma tumor suppressor protein (Rb) and other substrates. Surprisingly, purified and endogenous phosp27-CDK4-CycD1 complexes were insensitive to the CDK4-targeting drug palbociclib. Palbociclib instead primarily targeted monomeric CDK4 and CDK6 (CDK4/6) in breast tumor cells. Our data characterize phosp27-CDK4-CycD1 as an active Rb kinase that is refractory to clinically relevant CDK4/6 inhibitors.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA. srubin@ucsc.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
G1/S-specific cyclin-D1A249Homo sapiensMutation(s): 0 
Gene Names: CCND1BCL1PRAD1
UniProt & NIH Common Fund Data Resources
Find proteins for P24385 (Homo sapiens)
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Go to UniProtKB:  P24385
PHAROS:  P24385
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 4B302Homo sapiensMutation(s): 2 
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase inhibitor 1BC72Homo sapiensMutation(s): 3 
Gene Names: CDKN1BKIP1
UniProt & NIH Common Fund Data Resources
Find proteins for P46527 (Homo sapiens)
Explore P46527 
Go to UniProtKB:  P46527
PHAROS:  P46527
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.58α = 90
b = 66.73β = 90
c = 184.85γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesGM124148
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA206244

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release