7LT9 | pdb_00007lt9

Crystal structure of Ras suppressor-1 in complex with PINCH-1 LIM4-5 domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 
    0.234 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7LT9

This is version 1.3 of the entry. See complete history

Literature

Molecular basis for Ras suppressor-1 binding to PINCH-1 in focal adhesion assembly.

Fukuda, K.Lu, F.Qin, J.

(2021) J Biological Chem 296: 100685-100685

  • DOI: https://doi.org/10.1016/j.jbc.2021.100685
  • Primary Citation Related Structures: 
    7LT8, 7LT9

  • PubMed Abstract: 

    Ras suppressor-1 (Rsu-1) is a leucine-rich repeat (LRR)-containing protein that is crucial for regulating cell adhesion and is involved in such physiological and pathological processes as focal adhesion assembly and tumor metastasis. Rsu-1 interacts with zinc-finger type multi-LIM domain-containing adaptor protein PINCH-1, known to be involved in the integrin-mediated consensus adhesome, but not with its highly homologous family member PINCH-2. However, the structural basis for and regulatory mechanisms of this specific interaction remain unclear. Here, we determined the crystal structures of Rsu-1 and its complex with the PINCH-1 LIM4-5 domains. Rsu-1 displays an arc-shaped solenoid architecture, with eight LRRs shielded by N- and C-terminal capping modules. We showed that the conserved concave surface of the Rsu-1 LRR domain binds and stabilizes the PINCH-1 LIM5 domain via salt bridge and hydrophobic interactions, while the C-terminal non-LIM region of PINCH-2 sterically disfavors Rsu-1 binding. We also showed that Rsu-1 can be assembled, via PINCH-1-binding, into a heteropentamer complex comprising Rsu-1, PINCH-1, ILK, Parvin, and Kindlin-2, which constitute a major consensus integrin adhesome crucial for focal adhesion assembly. Our mutagenesis and cell biological data emphasize the significance of the Rsu-1/PINCH-1 interaction in focal adhesion assembly and cell spreading, providing crucial molecular insights into Rsu-1-mediated cell adhesion with implications for disease development.


  • Organizational Affiliation
    • Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Ohio, USA.

Macromolecule Content 

  • Total Structure Weight: 48.31 kDa 
  • Atom Count: 3,070 
  • Modeled Residue Count: 382 
  • Deposited Residue Count: 421 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ras suppressor protein 1280Homo sapiensMutation(s): 0 
Gene Names: RSU1RSP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15404 (Homo sapiens)
Explore Q15404 
Go to UniProtKB:  Q15404
PHAROS:  Q15404
GTEx:  ENSG00000148484 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15404
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LIM and senescent cell antigen-like-containing domain protein 1141Homo sapiensMutation(s): 0 
Gene Names: LIMS1PINCHPINCH1
UniProt & NIH Common Fund Data Resources
Find proteins for P48059 (Homo sapiens)
Explore P48059 
Go to UniProtKB:  P48059
PHAROS:  P48059
GTEx:  ENSG00000169756 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48059
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free:  0.234 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.042α = 90
b = 144.384β = 90
c = 185.691γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2021-07-21
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description