3QCW

Structure of neurexin 1 alpha (domains LNS1-LNS6), no splice inserts

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

The Structure of Neurexin 1 alpha Reveals Features Promoting a Role as Synaptic Organizer

Chen, F., Venugopal, V., Murray, B., Rudenko, G.

(2011) Structure 19: 779-789

  • DOI: 10.1016/j.str.2011.03.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • α-neurexins are essential synaptic adhesion molecules implicated in autism spectrum disorder and schizophrenia. The α-neurexin extracellular domain consists of six LNS domains interspersed by three EGF-like repeats and interacts with many different p ...

    α-neurexins are essential synaptic adhesion molecules implicated in autism spectrum disorder and schizophrenia. The α-neurexin extracellular domain consists of six LNS domains interspersed by three EGF-like repeats and interacts with many different proteins in the synaptic cleft. To understand how α-neurexins might function as synaptic organizers, we solved the structure of the neurexin 1α extracellular domain (n1α) to 2.65 Å. The L-shaped molecule can be divided into a flexible repeat I (LNS1-EGF-A-LNS2), a rigid horseshoe-shaped repeat II (LNS3-EGF-B-LNS4) with structural similarity to so-called reelin repeats, and an extended repeat III (LNS5-EGF-B-LNS6) with controlled flexibility. A 2.95 Å structure of n1α carrying splice insert SS#3 in LNS4 reveals that SS#3 protrudes as a loop and does not alter the rigid arrangement of repeat II. The global architecture imposed by conserved structural features enables α-neurexins to recruit and organize proteins in distinct and variable ways, influenced by splicing, thereby promoting synaptic function.

    Organizational Affiliation: 

    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neurexin-1-alpha
A, B
1245Bos taurusMutation(s): 1 
Gene Names: NRXN1
Find proteins for Q28146 (Bos taurus)
Go to Gene View: NRXN1
Go to UniProtKB:  Q28146
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 2.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 
  • Space Group: P 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/78 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 60.953α = 90.61
b = 114.543β = 90.87
c = 159.581γ = 92.18
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2011-01-17 
  • Released Date: 2011-06-15 
  • Deposition Author(s): Rudenko, G.

Revision History 

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-07-26
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-08
    Type: Refinement description