2XB6

Revisited crystal structure of Neurexin1beta-Neuroligin4 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Insights Into the Exquisite Selectivity of Neurexin-Neuroligin Synaptic Interactions

Leone, P.Comoletti, D.Ferracci, G.Conrod, S.Garcia, S.U.Taylor, P.Bourne, Y.Marchot, P.

(2010) EMBO J 29: 2461

  • DOI: 10.1038/emboj.2010.123
  • Primary Citation of Related Structures:  
    2XB6

  • PubMed Abstract: 
  • The extracellular domains of neuroligins and neurexins interact through Ca(2+) to form flexible trans-synaptic associations characterized by selectivity for neuroligin or neurexin subtypes. This heterophilic interaction, essential for synaptic matura ...

    The extracellular domains of neuroligins and neurexins interact through Ca(2+) to form flexible trans-synaptic associations characterized by selectivity for neuroligin or neurexin subtypes. This heterophilic interaction, essential for synaptic maturation and differentiation, is regulated by gene selection, alternative mRNA splicing and post-translational modifications. A new, 2.6 A-resolution crystal structure of a soluble neurexin-1beta-neuroligin-4 (Nrx1beta-NL4) complex permits a detailed description of the Ca(2+)-coordinated interface and unveils concerted positional rearrangements of several residues of NL4, not observed in neuroligin-1, associated with Nrx1beta binding. Surface plasmon resonance analysis of the binding of structure-guided Nrx1beta mutants towards NL4 and neuroligin-1 shows that flexibility of the Nrx1beta-binding site in NL4 is reflected in a greater dissociation constant of the complex and higher sensitivity to ionic strength and pH variations. Analysis of neuroligin mutants points to critical functions for two respective residues in neuroligin-1 and neuroligin-2 in governing the affinity of the complexes. Although neuroligin-1 and neuroligin-2 have pre-determined conformations that respectively promote and prevent Nrx1beta association, unique conformational reshaping of the NL4 surface is required to permit Nrx1beta association.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, CNRS/Université d'Aix-Marseille, Campus Luminy, Marseille, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEUROLIGIN-4, X-LINKEDAB588Homo sapiensMutation(s): 0 
Gene Names: NLGN4XKIAA1260NLGN4UNQ365/PRO701
Find proteins for Q8N0W4 (Homo sapiens)
Explore Q8N0W4 
Go to UniProtKB:  Q8N0W4
NIH Common Fund Data Resources
PHAROS  Q8N0W4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NEUREXIN-1-BETACD179Rattus norvegicusMutation(s): 0 
Gene Names: Nrxn1
Find proteins for Q63373 (Rattus norvegicus)
Explore Q63373 
Go to UniProtKB:  Q63373
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MES
Query on MES

Download CCD File 
C
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B, C
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.307α = 90
b = 198.779β = 90
c = 85.896γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2019-04-03
    Changes: Data collection, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary