3MW3 | pdb_00003mw3

Crystal structure of beta-neurexin 2 with the splice insert 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.252 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.3 of the entry. See complete history

Literature

Splice Form Dependence of beta-Neurexin/Neuroligin Binding Interactions.

Koehnke, J.Katsamba, P.S.Ahlsen, G.Bahna, F.Vendome, J.Honig, B.Shapiro, L.Jin, X.

(2010) Neuron 67: 61-74

  • DOI: https://doi.org/10.1016/j.neuron.2010.06.001
  • Primary Citation Related Structures: 
    3MW2, 3MW3, 3MW4

  • PubMed Abstract: 

    Alternatively spliced beta-neurexins (beta-NRXs) and neuroligins (NLs) are thought to have distinct extracellular binding affinities, potentially providing a beta-NRX/NL synaptic recognition code. We utilized surface plasmon resonance to measure binding affinities between all combinations of alternatively spliced beta-NRX 1-3 and NL 1-3 ectodomains. Binding was observed for all beta-NRX/NL pairs. The presence of the NL1 B splice insertion lowers beta-NRX binding affinity by approximately 2-fold, while beta-NRX splice insertion 4 has small effects that do not synergize with NL splicing. New structures of glycosylated beta-NRXs 1 and 2 containing splice insertion 4 reveal that the insertion forms a new beta strand that replaces the beta10 strand, leaving the NL binding site intact. This helps to explain the limited effect of splice insert 4 on NRX/NL binding affinities. These results provide new structural insights and quantitative binding information to help determine whether and how splice isoform choice plays a role in beta-NRX/NL-mediated synaptic recognition.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

Macromolecule Content 

  • Total Structure Weight: 23.57 kDa 
  • Atom Count: 1,650 
  • Modeled Residue Count: 189 
  • Deposited Residue Count: 208 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neurexin-2-beta208Rattus norvegicusMutation(s): 1 
Gene Names: Nrxn2
UniProt
Find proteins for Q63376 (Rattus norvegicus)
Explore Q63376 
Go to UniProtKB:  Q63376
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63376
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G16421CZ
GlyCosmos: G16421CZ
GlyGen: G16421CZ

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.252 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.657α = 90
b = 102.087β = 90
c = 78.512γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-10-06
    Changes: Advisory, Database references, Structure summary
  • Version 2.2: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-11-06
    Changes: Structure summary