6P8E

Crystal structure of CDK4 in complex with CyclinD1 and P27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.172 

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: 10.1126/science.aaw2106
  • Primary Citation of Related Structures:  

  • 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 ...

    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.,Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA.,Center for Personalized Medicine, Roswell Park Cancer Center, Buffalo, NY 14263, USA.,Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
G1/S-specific cyclin-D1
A
249Homo sapiensMutation(s): 0 
Gene Names: CCND1 (BCL1, PRAD1)
Find proteins for P24385 (Homo sapiens)
Go to Gene View: CCND1
Go to UniProtKB:  P24385
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 4
B
302Homo sapiensMutation(s): 2 
Gene Names: CDK4
EC: 2.7.11.22
Find proteins for P11802 (Homo sapiens)
Go to Gene View: CDK4
Go to UniProtKB:  P11802
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase inhibitor 1B
C
72Homo sapiensMutation(s): 0 
Gene Names: CDKN1B (KIP1)
Find proteins for P46527 (Homo sapiens)
Go to Gene View: CDKN1B
Go to UniProtKB:  P46527
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.172 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 62.410α = 90.00
b = 67.490β = 90.00
c = 187.280γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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