9LWX | pdb_00009lwx

Crystal structure of the Filamin A repeat 21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.268 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Filamin-AA [auth D],
B [auth A],
C [auth B],
D [auth C]
98Esselenichthys 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.268 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.694α = 78.421
b = 47.912β = 83.693
c = 50.36γ = 90.096
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

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