6ATH

Cdk2/cyclin A/p27-KID-deltaC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation.

Tsytlonok, M.Sanabria, H.Wang, Y.Felekyan, S.Hemmen, K.Phillips, A.H.Yun, M.K.Waddell, M.B.Park, C.G.Vaithiyalingam, S.Iconaru, L.White, S.W.Tompa, P.Seidel, C.A.M.Kriwacki, R.

(2019) Nat Commun 10: 1676-1676

  • DOI: 10.1038/s41467-019-09446-w

  • PubMed Abstract: 
  • p27 <sup>Kip1 </sup> is an intrinsically disordered protein (IDP) that inhibits cyclin-dependent kinase (Cdk)/cyclin complexes (e.g., Cdk2/cyclin A), causing cell cycle arrest. Cell division progresses when stably Cdk2/cyclin A-bound p27 is phosphory ...

    p27 Kip1 is an intrinsically disordered protein (IDP) that inhibits cyclin-dependent kinase (Cdk)/cyclin complexes (e.g., Cdk2/cyclin A), causing cell cycle arrest. Cell division progresses when stably Cdk2/cyclin A-bound p27 is phosphorylated on one or two structurally occluded tyrosine residues and a distal threonine residue (T187), triggering degradation of p27. Here, using an integrated biophysical approach, we show that Cdk2/cyclin A-bound p27 samples lowly-populated conformations that provide access to the non-receptor tyrosine kinases, BCR-ABL and Src, which phosphorylate Y88 or Y88 and Y74, respectively, thereby promoting intra-assembly phosphorylation (of p27) on distal T187. Even when tightly bound to Cdk2/cyclin A, intrinsic flexibility enables p27 to integrate and process signaling inputs, and generate outputs including altered Cdk2 activity, p27 stability, and, ultimately, cell cycle progression. Intrinsic dynamics within multi-component assemblies may be a general mechanism of signaling by regulatory IDPs, which can be subverted in human disease.


    Organizational Affiliation

    Department of Radiation Oncology, West Cancer Center and Research Institute, Memphis, TN, 38138, USA.,Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary. tompa@enzim.hu.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, 38163, USA. richard.kriwacki@stjude.org.,Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany. cseidel@hhu.de.,Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.,Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38103, USA.,Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. richard.kriwacki@stjude.org.,VIB Center for Structural Biology, Vrije Universiteit Brussel, Pleinlaan, 2 1050, Brussels, Belgium. tompa@enzim.hu.,VIB Center for Structural Biology, Vrije Universiteit Brussel, Pleinlaan, 2 1050, Brussels, Belgium.,Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225, Düsseldorf, Germany.,Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 2
A
300Homo 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
Cyclin-A2
B
263Homo sapiensMutation(s): 0 
Gene Names: CCNA2 (CCN1, CCNA)
Find proteins for P20248 (Homo sapiens)
Go to Gene View: CCNA2
Go to UniProtKB:  P20248
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase inhibitor 1B
C
68Homo 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.191α = 90.00
b = 77.645β = 90.00
c = 137.511γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-08-29 
  • Released Date: 2018-09-12 
  • Deposition Author(s): White, S.W., Yun, M.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01 CA82491, P30 CA21765

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2019-04-10
    Type: Data collection, Database references
  • Version 1.3: 2019-04-24
    Type: Data collection, Database references