6MIB

Crystal structure of the ILK ATP-binding deficient mutant (L207W)/alpha-parvin core complex

  • Classification: CELL ADHESION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2018-09-19 Released: 2018-11-07 
  • Deposition Author(s): Fukuda, K., Qin, J.
  • Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Non-catalytic signaling by pseudokinase ILK for regulating cell adhesion.

Vaynberg, J.Fukuda, K.Lu, F.Bialkowska, K.Chen, Y.Plow, E.F.Qin, J.

(2018) Nat Commun 9: 4465-4465

  • DOI: https://doi.org/10.1038/s41467-018-06906-7
  • Primary Citation of Related Structures:  
    6MIB, 6MIF

  • PubMed Abstract: 

    Dynamic communication between integrin-containing complexes (focal adhesions, FAs) and actin filaments is critical for regulating cell adhesion. Pseudokinase ILK plays a key role in this process but the underlying mechanism remains highly elusive. Here we show that by recruiting FA adaptors PINCH and Parvin into a heterotrimeric complex (IPP), ILK triggers F-actin filament bundling - a process known to generate force/mechanical signal to promote cytoskeleton reassembly and dynamic cell adhesion. Structural, biochemical, and functional analyses revealed that the F-actin bundling is orchestrated by two previously unrecognized WASP-Homology-2 actin binding motifs within IPP, one from PINCH and the other from Parvin. Strikingly, this process is also sensitized to Mg-ATP bound to the pseudoactive site of ILK and its dysregulation severely impairs stress fibers formation, cell spreading, and migration. These data identify a crucial mechanism for ILK, highlighting its uniqueness as a pseudokinase to transduce non-catalytic signal and regulate cell adhesion.


  • Organizational Affiliation

    Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin-linked protein kinase271Homo sapiensMutation(s): 1 
Gene Names: ILKILK1ILK2
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
GTEx:  ENSG00000166333 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13418
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-parvin129Homo sapiensMutation(s): 0 
Gene Names: PARVAMXRA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVD7 (Homo sapiens)
Explore Q9NVD7 
Go to UniProtKB:  Q9NVD7
PHAROS:  Q9NVD7
GTEx:  ENSG00000197702 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NVD7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.714α = 90
b = 117.635β = 114.54
c = 47.775γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references