2R16

Crystal Structure of bovine neurexin 1 alpha LNS/LG domain 4 (with no splice insert)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Regulation of Neurexin 1beta Tertiary Structure and Ligand Binding through Alternative Splicing

Shen, K.C.Kuczynska, D.A.Wu, I.J.Murray, B.H.Sheckler, L.R.Rudenko, G.

(2008) Structure 16: 422-431

  • DOI: https://doi.org/10.1016/j.str.2008.01.005
  • Primary Citation of Related Structures:  
    2R16, 2R1B, 2R1D

  • PubMed Abstract: 

    Neurexins and neuroligins play an essential role in synapse function, and their alterations are linked to autistic spectrum disorder. Interactions between neurexins and neuroligins regulate inhibitory and excitatory synaptogenesis in vitro through a "splice-insert signaling code." In particular, neurexin 1beta carrying an alternative splice insert at site SS#4 interacts with neuroligin 2 (found predominantly at inhibitory synapses) but much less so with other neuroligins (those carrying an insert at site B and prevalent at excitatory synapses). The structure of neurexin 1beta+SS#4 reveals dramatic rearrangements to the "hypervariable surface," the binding site for neuroligins. The splice insert protrudes as a long helix into space, triggers conversion of loop beta10-beta11 into a helix rearranging the binding site for neuroligins, and rearranges the Ca(2+)-binding site required for ligand binding, increasing its affinity. Our structures reveal the mechanism by which neurexin 1beta isoforms acquire neuroligin splice isoform selectivity.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neurexin-1-alpha182Bos taurusMutation(s): 0 
Gene Names: NRXN1
UniProt
Find proteins for Q28146 (Bos taurus)
Explore Q28146 
Go to UniProtKB:  Q28146
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ28146
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.322α = 90
b = 90.322β = 90
c = 39.624γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2008-03-25 
  • Deposition Author(s): Rudenko, G.

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description