Biological Assembly 1  

 3D View: Structure | Electron Density | 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: gel filtration

Macromolecule Content

• Total Structure Weight: 146.87 kDa 
• Atom Count: 8489 
• Modelled Residue Count: 1067 
• Deposited Residue Count: 1310 
• Unique protein chains: 1

7CEE

Crystal structure of mouse neuroligin-3

• DOI: 10.2210/pdb7CEE/pdb

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


• Deposited: 2020-06-23 Released: 2021-02-24 
• Deposition Author(s): Yamagata, A., Yoshida, T., Shiroshima, T., Maeda, A., Fukai, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 0.251 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice.

Yoshida, T., Yamagata, A., Imai, A., Kim, J., Izumi, H., Nakashima, S., Shiroshima, T., Maeda, A., Iwasawa-Okamoto, S., Azechi, K., Osaka, F., Saitoh, T., Maenaka, K., Shimada, T., Fukata, Y., Fukata, M., Matsumoto, J., Nishijo, H., Takao, K., Tanaka, S., Okabe, S., Tabuchi, K., Uemura, T., Mishina, M., Mori, H., Fukai, S.

(2021) Nat Commun 12: 1848-1848

• PubMed: 33758193 
• DOI: 10.1038/s41467-021-22059-6
• Primary Citation of Related Structures:  
  7CEG, 7CEE


• PubMed Abstract: 
  

Neuroligin 3 (NLGN3) and neurexins (NRXNs) constitute a canonical transsynaptic cell-adhesion pair, which has been implicated in autism. In autism spectrum disorder (ASD) development of sociality can be impaired. However, the molecular mechanism underlying NLGN3-mediated social development is unclear. Here, we identify non-canonical interactions between NLGN3 and protein tyrosine phosphatase δ (PTPδ) splice variants, competing with NRXN binding. NLGN3-PTPδ complex structure revealed a splicing-dependent interaction mode and competition mechanism between PTPδ and NRXNs. Mice carrying a NLGN3 mutation that selectively impairs NLGN3-NRXN interaction show increased sociability, whereas mice where the NLGN3-PTPδ interaction is impaired exhibit impaired social behavior and enhanced motor learning, with imbalance in excitatory/inhibitory synaptic protein expressions, as reported in the Nlgn3 R451C autism model. At neuronal level, the autism-related Nlgn3 R451C mutation causes selective impairment in the non-canonical pathway. Our findings suggest that canonical and non-canonical NLGN3 pathways compete and regulate the development of sociality.

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Organizational Affiliation: 

Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroligin-3	A, B	655	Mus musculus	Mutation(s): 0  Gene Names: Nlgn3
Find proteins for Q8BYM5 (Mus musculus) Explore Q8BYM5  Go to UniProtKB:  Q8BYM5
NIH Common Fund Data Resources
IMPC:  MGI:2444609

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 0.251 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.842	α = 90
b = 167.142	β = 90
c = 177.95	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-06-23 
• Released Date: 2021-02-24 
Deposition Author(s): Yamagata, A., Yoshida, T., Shiroshima, T., Maeda, A., Fukai, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP16H04749
Japan Society for the Promotion of Science (JSPS)	Japan	JP25293057
Japan Society for the Promotion of Science (JSPS)	Japan	JP24247014
Japan Science and Technology	Japan	JPMJCR12M5

Revision History  

• Version 1.0: 2021-02-24
  Type: Initial release
  
• Version 1.1: 2021-04-07
  Changes: Database references