7CEE

Crystal structure of mouse neuroligin-3


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan. fukai@kuchem.kyoto-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neuroligin-3 AB655Mus musculusMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, B
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: 2.76 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 = 65.842α = 90
b = 167.142β = 90
c = 177.95γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP16H04749
Japan Society for the Promotion of Science (JSPS)JapanJP25293057
Japan Society for the Promotion of Science (JSPS)JapanJP24247014
Japan Science and TechnologyJapanJPMJCR12M5

Revision History  (Full details and data files)

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