6PNP

Crystal structure of the splice insert-free neurexin-1 LNS2 domain in complex with neurexophilin-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.203 

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This is version 1.4 of the entry. See complete history


Literature

Structures of neurexophilin-neurexin complexes reveal a regulatory mechanism of alternative splicing.

Wilson, S.C.White, K.I.Zhou, Q.Pfuetzner, R.A.Choi, U.B.Sudhof, T.C.Brunger, A.T.

(2019) EMBO J 38: e101603-e101603

  • DOI: https://doi.org/10.15252/embj.2019101603
  • Primary Citation of Related Structures:  
    6PNP, 6PNQ

  • PubMed Abstract: 

    Neurexins are presynaptic, cell-adhesion molecules that specify the functional properties of synapses via interactions with trans-synaptic ligands. Neurexins are extensively alternatively spliced at six canonical sites that regulate multifarious ligand interactions, but the structural mechanisms underlying alternative splicing-dependent neurexin regulation are largely unknown. Here, we determined high-resolution structures of the complex of neurexophilin-1 and the second laminin/neurexin/sex-hormone-binding globulin domain (LNS2) of neurexin-1 and examined how alternative splicing at splice site #2 (SS2) regulates the complex. Our data reveal a unique, extensive, neurexophilin-neurexin binding interface that extends the jelly-roll β-sandwich of LNS2 of neurexin-1 into neurexophilin-1. The SS2A insert of LNS2 augments this interface, increasing the binding affinity of LNS2 for neurexophilin-1. Taken together, our data reveal an unexpected architecture of neurexophilin-neurexin complexes that accounts for the modulation of binding by alternative splicing, which in turn regulates the competition of neurexophilin for neurexin binding with other ligands.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neurexin-1194Mus musculusMutation(s): 1 
Gene Names: Nrxn1Kiaa0578
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CS84 (Mus musculus)
Explore Q9CS84 
Go to UniProtKB:  Q9CS84
IMPC:  MGI:1096391
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CS84
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neurexophilin-1168Rattus norvegicusMutation(s): 3 
Gene Names: Nxph1Nph1
UniProt
Find proteins for Q63366 (Rattus norvegicus)
Explore Q63366 
Go to UniProtKB:  Q63366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63366
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.705α = 90
b = 60.983β = 106.74
c = 79.619γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesR37MH63105
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-11-27
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description