5UQ3

Crystal structure of human Cdk2-Spy1-P27 ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of divergent cyclin-dependent kinase activation by Spy1/RINGO proteins.

McGrath, D.A.Fifield, B.A.Marceau, A.H.Tripathi, S.Porter, L.A.Rubin, S.M.

(2017) EMBO J. 36: 2251-2262

  • DOI: 10.15252/embj.201796905
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cyclin-dependent kinases (Cdks) are principal drivers of cell division and are an important therapeutic target to inhibit aberrant proliferation. Cdk enzymatic activity is tightly controlled through cyclin interactions, posttranslational modification ...

    Cyclin-dependent kinases (Cdks) are principal drivers of cell division and are an important therapeutic target to inhibit aberrant proliferation. Cdk enzymatic activity is tightly controlled through cyclin interactions, posttranslational modifications, and binding of inhibitors such as the p27 tumor suppressor protein. Spy1/RINGO (Spy1) proteins bind and activate Cdk but are resistant to canonical regulatory mechanisms that establish cell-cycle checkpoints. Cancer cells exploit Spy1 to stimulate proliferation through inappropriate activation of Cdks, yet the mechanism is unknown. We have determined crystal structures of the Cdk2-Spy1 and p27-Cdk2-Spy1 complexes that reveal how Spy1 activates Cdk. We find that Spy1 confers structural changes to Cdk2 that obviate the requirement of Cdk activation loop phosphorylation. Spy1 lacks the cyclin-binding site that mediates p27 and substrate affinity, explaining why Cdk-Spy1 is poorly inhibited by p27 and lacks specificity for substrates with cyclin-docking sites. We identify mutations in Spy1 that ablate its ability to activate Cdk2 and to proliferate cells. Our structural description of Spy1 provides important mechanistic insights that may be utilized for targeting upregulated Spy1 in cancer.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 2
A
301Homo sapiensMutation(s): 0 
Gene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Speedy protein A
B
160Homo sapiensMutation(s): 0 
Gene Names: SPDYA (SPDY1, SPY1)
Find proteins for Q5MJ70 (Homo sapiens)
Go to Gene View: SPDYA
Go to UniProtKB:  Q5MJ70
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase inhibitor 1B
C
201Homo sapiensMutation(s): 0 
Gene Names: CDKN1B (KIP1)
Find proteins for P46527 (Homo sapiens)
Go to Gene View: CDKN1B
Go to UniProtKB:  P46527
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.243 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 124.650α = 90.00
b = 124.650β = 90.00
c = 88.490γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Database references