Crystal Structure of the Immunoglobulin variable domain of Nectin-2

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

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Structure of Nectin-2 reveals determinants of homophilic and heterophilic interactions that control cell-cell adhesion.

Samanta, D.Ramagopal, U.A.Rubinstein, R.Vigdorovich, V.Nathenson, S.G.Almo, S.C.

(2012) Proc Natl Acad Sci U S A 109: 14836-14840

  • DOI: https://doi.org/10.1073/pnas.1212912109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Nectins are members of the Ig superfamily that mediate cell-cell adhesion through homophilic and heterophilic interactions. We have determined the crystal structure of the nectin-2 homodimer at 1.3 Å resolution. Structural analysis and complementary mutagenesis studies reveal the basis for recognition and selectivity among the nectin family members. Notably, the close proximity of charged residues at the dimer interface is a major determinant of the binding affinities associated with homophilic and heterophilic interactions within the nectin family. Our structural and biochemical data provide a mechanistic basis to explain stronger heterophilic versus weaker homophilic interactions among these family members and also offer insights into nectin-mediated transinteractions between engaging cells.

  • Organizational Affiliation

    Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poliovirus receptor-related protein 2128Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92692 (Homo sapiens)
Explore Q92692 
Go to UniProtKB:  Q92692
PHAROS:  Q92692
GTEx:  ENSG00000130202 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92692
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.964α = 90
b = 57.964β = 90
c = 67.544γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-3000data reduction

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-09-05
    Changes: Database references
  • Version 1.3: 2012-09-12
    Changes: Structure summary
  • Version 1.4: 2012-10-03
    Changes: Database references
  • Version 1.5: 2012-11-07
    Changes: Data collection