9AZ3 | pdb_00009az3

Cryo-EM reveals molecular mechanisms underlying the inhibitory effect of netrin-4 on laminin matrix formation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM reveals molecular mechanisms underlying the inhibitory effect of netrin-4 on laminin matrix formation.

Kulczyk, A.W.McKee, K.K.Yurchenco, P.D.

(2025) Nat Commun 16: 7256-7256

  • DOI: https://doi.org/10.1038/s41467-025-62814-7
  • Primary Citation of Related Structures:  
    9AZ3

  • PubMed Abstract: 

    Netrin-4 is a tumor suppressor that interferes with formation of the laminin lattice. We employed cryo-electron microscopy to determine a structure of the protein complex consisting of the N-terminal fragments from netrin-4 and laminin γ1. The structure reveals that netrin-4 binds laminin γ1 at the molecular interface where laminin β1 would have bound, thus inhibiting the assembly of the heterotrimeric laminin polymer nodes consisting of α1, β1, and γ1 subunits, and their polymerization into the extracellular lattice. The four orders of magnitude higher affinity of the netrin-4-laminin γ1 interaction results from the larger buried surface area than the one formed by β1 and γ1 laminins and greater electrostatic surface complementarity. Our findings, supported by site-directed mutagenesis, solid-phase binding analysis, laminin polymerization, and Schwann cell assays, collectively demonstrate that, in addition to inhibiting laminin polymerization, netrin-4 disassembles the pre-existing laminin lattice. The structure has the potential to facilitate the development of novel therapies for cancer treatment.


  • Organizational Affiliation
    • Institute for Quantitative Biomedicine, Department of Biochemistry and Microbiology, Rutgers University, Piscataway, NJ, USA. arek.kulczyk@rutgers.edu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Laminin subunit gamma-1A [auth G]305Homo sapiensMutation(s): 0 
Gene Names: LAMC1LAMB2
UniProt & NIH Common Fund Data Resources
Find proteins for P11047 (Homo sapiens)
Explore P11047 
Go to UniProtKB:  P11047
PHAROS:  P11047
GTEx:  ENSG00000135862 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11047
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Netrin-4B [auth N]284Mus musculusMutation(s): 0 
Gene Names: Ntn4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9JI33 (Mus musculus)
Explore Q9JI33 
Go to UniProtKB:  Q9JI33
IMPC:  MGI:1888978
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JI33
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release