6P8E

Crystal structure of CDK4 in complex with CyclinD1 and P27

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


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

  • 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-D1249Homo sapiensMutation(s): 0 
Gene Names: CCND1, BCL1, PRAD1
UniProt & NIH Common Fund Data Resources
Find proteins for P24385 (Homo sapiens)
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Go to UniProtKB:  P24385
PHAROS:  P24385
Entity Groups  
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UniProt GroupP24385
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 4302Homo 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
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UniProt GroupP11802
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase inhibitor 1B72Homo sapiensMutation(s): 0 
Gene Names: CDKN1B, KIP1, p27
UniProt & NIH Common Fund Data Resources
Find proteins for P46527 (Homo sapiens)
Explore P46527 
Go to UniProtKB:  P46527
PHAROS:  P46527
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UniProt GroupP46527
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth B],
E [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.41α = 90
b = 67.49β = 90
c = 187.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

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