3B3Q

Crystal structure of a synaptic adhesion complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for synaptic adhesion mediated by neuroligin-neurexin interactions.

Chen, X.Liu, H.Shim, A.H.Focia, P.J.He, X.

(2008) Nat.Struct.Mol.Biol. 15: 50-56

  • DOI: 10.1038/nsmb1350

  • PubMed Abstract: 
  • The heterophilic synaptic adhesion molecules neuroligins and neurexins are essential for establishing and maintaining neuronal circuits by modulating the formation and maturation of synapses. The neuroligin-neurexin adhesion is Ca2+-dependent and reg ...

    The heterophilic synaptic adhesion molecules neuroligins and neurexins are essential for establishing and maintaining neuronal circuits by modulating the formation and maturation of synapses. The neuroligin-neurexin adhesion is Ca2+-dependent and regulated by alternative splicing. We report a structure of the complex at a resolution of 2.4 A between the mouse neuroligin-1 (NL1) cholinesterase-like domain and the mouse neurexin-1beta (NX1beta) LNS (laminin, neurexin and sex hormone-binding globulin-like) domain. The structure revealed a delicate neuroligin-neurexin assembly mediated by a hydrophilic, Ca2+-mediated and solvent-supplemented interface, rendering it capable of being modulated by alternative splicing and other regulatory factors. Thermodynamic data supported a mechanism wherein splicing site B of NL1 acts by modulating a salt bridge at the edge of the NL1-NX1beta interface. Mapping neuroligin mutations implicated in autism indicated that most such mutations are structurally destabilizing, supporting deficient neuroligin biosynthesis and processing as a common cause for this brain disorder.


    Organizational Affiliation

    Northwestern University Feinberg School of Medicine, Department of Molecular Pharmacology & Biological Chemistry, Searle 8-417, 303 East Chicago Avenue, Chicago, Illinois 60611, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nlgn1 protein
A, B
577Mus musculusGene Names: Nlgn1 (Kiaa1070)
Find proteins for Q99K10 (Mus musculus)
Go to UniProtKB:  Q99K10
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NRXN1 protein
E, F
197Homo sapiensGene Names: NRXN1
Find proteins for P58400 (Homo sapiens)
Go to Gene View: NRXN1
Go to UniProtKB:  P58400
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 116.590α = 90.00
b = 125.400β = 90.00
c = 131.860γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2013-05-15
    Type: Structure summary