2VAJ | pdb_00002vaj

Crystal structure of NCAM2 Ig1 (I4122 cell unit)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.268 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Crystal Structure of the Ig1 Domain of the Neural Cell Adhesion Molecule Ncam2 Displays Domain Swapping.

Rasmussen, K.K.Kulahin, N.Kristensen, O.Poulsen, J.C.Sigurskjold, B.W.Kastrup, J.S.Berezin, V.Bock, E.Walmod, P.S.Gajhede, M.

(2008) J Mol Biology 382: 1113

  • DOI: https://doi.org/10.1016/j.jmb.2008.07.084
  • Primary Citation Related Structures: 
    2VAJ

  • PubMed Abstract: 

    The crystal structure of the first immunoglobulin (Ig1) domain of neural cell adhesion molecule 2 (NCAM2/OCAM/RNCAM) is presented at a resolution of 2.7 A. NCAM2 is a member of the immunoglobulin superfamily of cell adhesion molecules (IgCAMs). In the structure, two Ig domains interact by domain swapping, as the two N-terminal beta-strands are interchanged. beta-Strand swapping at the terminal domain is the accepted mechanism of homophilic interactions amongst the cadherins, another class of CAMs, but it has not been observed within the IgCAM superfamily. Gel-filtration chromatography demonstrated the ability of NCAM2 Ig1 to form dimers in solution. Taken together, these observations suggest that beta-strand swapping could have a role in the molecular mechanism of homophilic binding for NCAM2.


  • Organizational Affiliation
    • Protein Laboratory, Department of Neuroscience and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark.

Macromolecule Content 

  • Total Structure Weight: 10.36 kDa 
  • Atom Count: 734 
  • Modeled Residue Count: 93 
  • Deposited Residue Count: 93 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NEURAL CELL ADHESION MOLECULE 293Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O15394 (Homo sapiens)
Explore O15394 
Go to UniProtKB:  O15394
PHAROS:  O15394
GTEx:  ENSG00000154654 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15394
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.268 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.279α = 90
b = 47.279β = 90
c = 196.727γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary