3F6Q

Crystal structure of integrin-linked kinase ankyrin repeat domain in complex with PINCH1 LIM1 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structural basis of integrin-linked kinase-PINCH interactions.

Chiswell, B.P.Zhang, R.Murphy, J.W.Boggon, T.J.Calderwood, D.A.

(2008) Proc.Natl.Acad.Sci.USA 105: 20677-20682

  • DOI: 10.1073/pnas.0811415106

  • PubMed Abstract: 
  • The heterotrimeric complex between integrin-linked kinase (ILK), PINCH, and parvin is an essential signaling platform, serving as a convergence point for integrin and growth-factor signaling and regulating cell adhesion, spreading, and migration. We ...

    The heterotrimeric complex between integrin-linked kinase (ILK), PINCH, and parvin is an essential signaling platform, serving as a convergence point for integrin and growth-factor signaling and regulating cell adhesion, spreading, and migration. We report a 1.6-A crystal structure of the ILK ankyrin repeat domain bound to the PINCH1 LIM1 domain, revealing the molecular basis of ILK-PINCH interactions and providing a structural description of this region of ILK. This structure identifies 5 ankyrin repeats in ILK, explains previous deletion mutagenesis data, permits identification of ILK and PINCH1 point mutations that disrupt the interaction, shows how zincs are coordinated by PINCH1 LIM1, and suggests that conformational flexibility and twisting between the 2 zinc fingers within the LIM1 domain may be important for ILK binding. These data provide an atomic-resolution description of a key interaction in the ILK-PINCH-parvin scaffolding complex.


    Organizational Affiliation

    Department of Pharmacology, Yale Cancer Center and Interdepartmental Program in Vascular Biology and Transplantation, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin-linked protein kinase
A
179Homo sapiensMutation(s): 0 
Gene Names: ILK (ILK1, ILK2)
EC: 2.7.11.1
Find proteins for Q13418 (Homo sapiens)
Go to Gene View: ILK
Go to UniProtKB:  Q13418
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LIM and senescent cell antigen-like-containing domain protein 1
B
72Homo sapiensMutation(s): 0 
Gene Names: LIMS1 (PINCH, PINCH1)
Find proteins for P48059 (Homo sapiens)
Go to Gene View: LIMS1
Go to UniProtKB:  P48059
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.161 
  • Space Group: P 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/554 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 37.004α = 78.01
b = 41.500β = 68.98
c = 46.469γ = 85.91
Software Package:
Software NamePurpose
ARP/wARPmodel building
PDB_EXTRACTdata extraction
DENZOdata reduction
CrystalCleardata collection
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance