9LXG | pdb_00009lxg

Filamin A repeat 21 in complex with LARP4 Ala269-Asn281 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 
    0.259 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9LXG

This is version 1.1 of the entry. See complete history

Literature

Structural Basis of the LARP4-Filamin A Interaction and Competition with Integrin beta 7 Tails.

Mao, Z.Ding, Y.Liu, Y.Mei, K.Nakamura, F.

(2025) J Mol Biology 437: 169262-169262

  • DOI: https://doi.org/10.1016/j.jmb.2025.169262
  • Primary Citation Related Structures: 
    9LWX, 9LXG

  • PubMed Abstract: 

    Filamin A (FLNA) is an actin cross-linking protein that connects multiple transmembrane receptors and cytosolic signaling proteins to regulate cell shape, motility, and signaling. Our previous report has shown that FLNA interacts directly with the La-related protein 4 (LARP4) and this interaction is essential for cell migration. Here, using the x-ray crystallography and protein-protein interaction studies, we investigated the molecular basis of LARP4 binding to FLNA. We described the high-resolution structure of the FLNA immunoglobulin-like repeat 21 (R21) and its complex with the LARP4 peptide. The FLNA-binding site in LARP4 is localized between Ala269 and Asn281, where it forms an extended β strand that interacts with the cleft formed by β strands C and D of FLNA R21. Consistent with this structure, the A279Cfs*2 mutation found in catalogue of somatic mutations in cancer (COSMIC) database and the experimentally introduced F277A mutation both disrupt LARP4 binding to FLNA. In contrast, the COSMIC-listed N275S mutation alters LARP4 membrane localization without affecting FLNA interaction, suggesting distinct functional outcomes. Cell migration assays showed that LARP4-knockdown cells expressing FLNA-binding-deficient mutants migrated faster than those expressing wild-type LARP4. The LARP4-binding site on FLNA overlaps with the β-integrin tail-binding region, and in vitro assays revealed that LARP4 can compete with integrin β7 tails for FLNA R21 binding. These results suggest that the LARP4-FLNA interaction may regulate cell migration, at least in part, by competing with integrin tails, although this mechanism has yet to be confirmed in vivo.


  • Organizational Affiliation
    • School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.

Macromolecule Content 

  • Total Structure Weight: 11.68 kDa 
  • Atom Count: 812 
  • Modeled Residue Count: 109 
  • Deposited Residue Count: 114 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Filamin-A101Esselenichthys carliMutation(s): 0 
Gene Names: FLNAFLNFLN1
UniProt & NIH Common Fund Data Resources
Find proteins for P21333 (Homo sapiens)
Explore P21333 
Go to UniProtKB:  P21333
PHAROS:  P21333
GTEx:  ENSG00000196924 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21333
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
La-related protein 413Esselenichthys carliMutation(s): 0 
Gene Names: Larp4
UniProt
Find proteins for Q8BWW4 (Mus musculus)
Explore Q8BWW4 
Go to UniProtKB:  Q8BWW4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BWW4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free:  0.259 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.04α = 90
b = 78.04β = 90
c = 32.36γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32070777

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references