3M45

Crystal structure of Ig1 domain of mouse SynCAM 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 
    0.245 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

N-glycosylation at the SynCAM (synaptic cell adhesion molecule) immunoglobulin interface modulates synaptic adhesion.

Fogel, A.I.Li, Y.Giza, J.Wang, Q.Lam, T.T.Modis, Y.Biederer, T.

(2010) J Biol Chem 285: 34864-34874

  • DOI: https://doi.org/10.1074/jbc.M110.120865
  • Primary Citation of Related Structures:  
    3M45

  • PubMed Abstract: 

    Select adhesion molecules connect pre- and postsynaptic membranes and organize developing synapses. The regulation of these trans-synaptic interactions is an important neurobiological question. We have previously shown that the synaptic cell adhesion molecules (SynCAMs) 1 and 2 engage in homo- and heterophilic interactions and bridge the synaptic cleft to induce presynaptic terminals. Here, we demonstrate that site-specific N-glycosylation impacts the structure and function of adhesive SynCAM interactions. Through crystallographic analysis of SynCAM 2, we identified within the adhesive interface of its Ig1 domain an N-glycan on residue Asn(60). Structural modeling of the corresponding SynCAM 1 Ig1 domain indicates that its glycosylation sites Asn(70)/Asn(104) flank the binding interface of this domain. Mass spectrometric and mutational studies confirm and characterize the modification of these three sites. These site-specific N-glycans affect SynCAM adhesion yet act in a differential manner. Although glycosylation of SynCAM 2 at Asn(60) reduces adhesion, N-glycans at Asn(70)/Asn(104) of SynCAM 1 increase its interactions. The modification of SynCAM 1 with sialic acids contributes to the glycan-dependent strengthening of its binding. Functionally, N-glycosylation promotes the trans-synaptic interactions of SynCAM 1 and is required for synapse induction. These results demonstrate that N-glycosylation of SynCAM proteins differentially affects their binding interface and implicate post-translational modification as a mechanism to regulate trans-synaptic adhesion.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell adhesion molecule 2
A, B, C, D
108Mus musculusMutation(s): 0 
Gene Names: Cadm2Igsf4dNecl3SynCAM 2
UniProt
Find proteins for Q8BLQ9 (Mus musculus)
Explore Q8BLQ9 
Go to UniProtKB:  Q8BLQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BLQ9
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q8BLQ9-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.245 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.847α = 75.91
b = 50.528β = 77.02
c = 79.851γ = 65.18
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-06
    Changes: Structure summary