6TL8

Structural basis of SALM3 dimerization and adhesion complex formation with the presynaptic receptor protein tyrosine phosphatases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.263 

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Ligand Structure Quality Assessment 


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Literature

Structural basis of SALM3 dimerization and synaptic adhesion complex formation with PTP sigma.

Karki, S.Shkumatov, A.V.Bae, S.Kim, H.Ko, J.Kajander, T.

(2020) Sci Rep 10: 11557-11557

  • DOI: 10.1038/s41598-020-68502-4
  • Primary Citation of Related Structures:  
    6TL8

  • PubMed Abstract: 
  • Synaptic adhesion molecules play an important role in the formation, maintenance and refinement of neuronal connectivity. Recently, several leucine rich repeat (LRR) domain containing neuronal adhesion molecules have been characterized including netrin G-ligands, SLITRKs and the synaptic adhesion-like molecules (SALMs) ...

    Synaptic adhesion molecules play an important role in the formation, maintenance and refinement of neuronal connectivity. Recently, several leucine rich repeat (LRR) domain containing neuronal adhesion molecules have been characterized including netrin G-ligands, SLITRKs and the synaptic adhesion-like molecules (SALMs). Dysregulation of these adhesion molecules have been genetically and functionally linked to various neurological disorders. Here we investigated the molecular structure and mechanism of ligand interactions for the postsynaptic SALM3 adhesion protein with its presynaptic ligand, receptor protein tyrosine phosphatase σ (PTPσ). We solved the crystal structure of the dimerized LRR domain of SALM3, revealing the conserved structural features and mechanism of dimerization. Furthermore, we determined the complex structure of SALM3 with PTPσ using small angle X-ray scattering, revealing a 2:2 complex similar to that observed for SALM5. Solution studies unraveled additional flexibility for the complex structure, but validated the uniform mode of action for SALM3 and SALM5 to promote synapse formation. The relevance of the key interface residues was further confirmed by mutational analysis with cellular binding assays and artificial synapse formation assays. Collectively, our results suggest that SALM3 dimerization is a pre-requisite for the SALM3-PTPσ complex to exert synaptogenic activity.


    Organizational Affiliation

    Institute of Biotechnology, University of Helsinki, Viikinkaari 1, PO Box 65, 00014, Helsinki, Finland. tommi.kajander@helsinki.fi.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Myeloid cell surface antigen CD33,Leucine-rich repeat and fibronectin type-III domain-containing protein 4A, B, C, D299Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: CD33SIGLEC3Lrfn4Salm3
UniProt & NIH Common Fund Data Resources
Find proteins for P20138 (Homo sapiens)
Explore P20138 
Go to UniProtKB:  P20138
PHAROS:  P20138
GTEx:  ENSG00000105383 
Find proteins for Q80XU8 (Mus musculus)
Explore Q80XU8 
Go to UniProtKB:  Q80XU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP20138Q80XU8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
E [auth C],
F [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.263 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.45α = 90
b = 132.16β = 90.08
c = 134.18γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Jane and Aatos Erkko FoundationFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary