Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 130.95 kDa 
• Atom Count: 7304 
• Modelled Residue Count: 1010 
• Deposited Residue Count: 1196 
• Unique protein chains: 1

6TL8

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

• PDB DOI: 10.2210/pdb6TL8/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2019-12-02 Released: 2020-07-22 
• Deposition Author(s): Karki, S., Shkumatov, A.V., Bae, S., Ko, J., Kajander, T.
• Funding Organization(s): Jane and Aatos Erkko Foundation

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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 

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

• PubMed: 32665594 
• 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). 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.

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Organizational Affiliation: 

Institute of Biotechnology, University of Helsinki, Viikinkaari 1, PO Box 65, 00014, Helsinki, Finland. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloid cell surface antigen CD33,Leucine-rich repeat and fibronectin type-III domain-containing protein 4	A, B, C, D	299	Homo sapiens, Mus musculus This entity is chimeric	Mutation(s): 0  Gene Names: CD33, SIGLEC3, Lrfn4, Salm3
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
UniProt Groups	P20138Q80XU8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth C], F [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 31.45	α = 90
b = 132.16	β = 90.08
c = 134.18	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-12-02 
• Released Date: 2020-07-22 
Deposition Author(s): Karki, S., Shkumatov, A.V., Bae, S., Ko, J., Kajander, T.

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Funding Organization	Location	Grant Number
Jane and Aatos Erkko Foundation	Finland	--

Revision History  

• 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