7V1A | pdb_00007v1a

Stapled TBS peptide from RIAM bound to talin R7R8 domains

  • Classification: CELL ADHESION
  • Organism(s): Mus musculus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-05-11 Released: 2023-06-14 
  • Deposition Author(s): Zhang, P., Gao, T., Wu, J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.254 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7V1A

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Inhibition of talin-induced integrin activation by a double-hit stapled peptide.

Gao, T.Cho, E.A.Zhang, P.Wu, J.

(2023) Structure 31: 948

  • DOI: https://doi.org/10.1016/j.str.2023.05.016
  • Primary Citation Related Structures: 
    7V1A

  • PubMed Abstract: 

    Integrins are ubiquitously expressed cell-adhesion proteins. Activation of integrins is triggered by talin through an inside-out signaling pathway, which can be driven by RAP1-interacting adaptor molecule (RIAM) through its interaction with talin at two distinct sites. A helical talin-binding segment (TBS) in RIAM interacts with both sites in talin, leading to integrin activation. The bispecificity inspires a "double-hit" strategy for inhibiting talin-induced integrin activation. We designed an experimental peptidomimetic inhibitor, S-TBS, derived from TBS and containing a molecular staple, which leads to stronger binding to talin and inhibition of talin:integrin interaction. The crystallographic study validates that S-TBS binds to the talin rod through the same interface as TBS. Moreover, the helical S-TBS exhibits excellent cell permeability and effectively suppresses integrin activation in cells in a talin-dependent manner. Our results shed light on a new class of integrin inhibitors and a novel approach to design multi-specific peptidomimetic inhibitors.


  • Organizational Affiliation
    • Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.

Macromolecule Content 

  • Total Structure Weight: 33.85 kDa 
  • Atom Count: 2,468 
  • Modeled Residue Count: 319 
  • Deposited Residue Count: 320 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Talin-1301Mus musculusMutation(s): 0 
Gene Names: Tln1Tln
UniProt
Find proteins for P26039 (Mus musculus)
Explore P26039 
Go to UniProtKB:  P26039
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26039
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ASP-ILE-ASP-GLN-MET-PHE-SER-THR-LEU-LEU-GLY-GLU-MK8-ASP-LEU-LEU-MK8-GLN-SER19Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8R5A3 (Mus musculus)
Explore Q8R5A3 
Go to UniProtKB:  Q8R5A3
IMPC:  MGI:1861354
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8R5A3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
(Subject of Investigation/LOI)

Query on EDO



Download:Ideal Coordinates CCD File
C [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MK8
Query on MK8
B
L-PEPTIDE LINKINGC7 H15 N O2LEU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.254 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.864α = 90
b = 104.334β = 90
c = 48.233γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States119560

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references
  • Version 1.2: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-25
    Changes: Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection
  • Version 1.5: 2024-10-16
    Changes: Structure summary