Crystal structure of mouse SALM5 adhesion protein extracellular LRR-Ig domain fragment

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report

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The structure of SALM5 suggests a dimeric assembly for the presynaptic RPTP ligand recognition.

Karki, S.Paudel, P.Sele, C.Shkumatov, A.V.Kajander, T.

(2018) Protein Eng Des Sel 31: 147-157

  • DOI: https://doi.org/10.1093/protein/gzy012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Synaptic adhesion molecules play a crucial role in the regulation of synapse development and maintenance. Recently, several families of leucine-rich repeat (LRR) domain-containing neuronal adhesion molecules have been characterised, including netrin-G ligands, LRRTMs and the synaptic adhesion-like molecule (SALM) family proteins. Most of these are expressed at the excitatory glutamatergic synapses, and dysfunctions of these genes are genetically linked with cognitive disorders, such as autism spectrum disorders and schizophrenia. The SALM family proteins SALM3 and SALM5, similar to SLITRKs, have been shown to bind to the presynaptic receptor protein tyrosine phosphatase (RPTP) family ligands. Here, we present the 3.1 Å crystal structure of the SALM5 LRR-Ig-domain construct and biophysical studies that verify the crystallographic results. We show that SALM1, SALM3 and SALM5 form similar dimeric structures, in which the LRR domains form the dimer interface. Both SALM3 and SALM5 bind to RPTP immunoglobulin domains with micromolar affinity. SALM3 shows a clear preference for the RPTP ligands with the meB splice insert. Our structural studies and sequence conservation analysis suggests a ligand-binding site and mechanism for RPTP binding via the dimeric LRR domain region.

  • Organizational Affiliation

    Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat and fibronectin type-III domain-containing protein 5388Mus musculusMutation(s): 0 
Gene Names: Lrfn5Kiaa4208Salm5
UniProt & NIH Common Fund Data Resources
Find proteins for Q8BXA0 (Mus musculus)
Explore Q8BXA0 
Go to UniProtKB:  Q8BXA0
IMPC:  MGI:2144814
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BXA0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 254.015α = 90
b = 254.015β = 90
c = 254.015γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Academy of FinlandFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references