3F6Q

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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 U S A 105: 20677-20682

  • DOI: 10.1073/pnas.0811415106
  • Primary Citation of Related Structures:  
    3F6Q

  • 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 report a 1 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin-linked protein kinaseA179Homo sapiensMutation(s): 0 
Gene Names: ILK, ILK1, ILK2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13418 (Homo sapiens)
Explore Q13418 
Go to UniProtKB:  Q13418
PHAROS:  Q13418
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13418
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LIM and senescent cell antigen-like-containing domain protein 1B72Homo sapiensMutation(s): 0 
Gene Names: LIMS1, PINCH, PINCH1
UniProt & NIH Common Fund Data Resources
Find proteins for P48059 (Homo sapiens)
Explore P48059 
Go to UniProtKB:  P48059
PHAROS:  P48059
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48059
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
W [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
T [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
U [auth B],
V [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 1
  • Diffraction Data DOI: 10.15785/SBGRID/554
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.004α = 78.01
b = 41.5β = 68.98
c = 46.469γ = 85.91
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
ARP/wARPmodel building

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

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