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Structural evidence for evolution of shark Ig new antigen receptor variable domain antibodies from a cell-surface receptor

Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12444-9. doi: 10.1073/pnas.0403509101. Epub 2004 Aug 10.

Abstract

The Ig new antigen receptors (IgNARs) are single-domain antibodies found in the serum of sharks. Here, we report 2.2- and 2.8-A structures of the type 2 IgNAR variable domains 12Y-1 and 12Y-2. Structural features include, first, an Ig superfamily topology transitional between cell adhesion molecules, antibodies, and T cell receptors; and, second, a vestigial complementarity-determining region 2 at the "bottom" of the molecule, apparently discontinuous from the antigen-binding paratope and similar to that observed in cell adhesion molecules. Thus, we suggest that IgNARs originated as cell-surface adhesion molecules coopted to the immune repertoire and represent an evolutionary lineage independent of variable heavy chain/variable light chain type antibodies. Additionally, both 12Y-1 and 12Y-2 form unique crystallographic dimers, predominantly mediated by main-chain framework interactions, which represent a possible model for primordial cell-based interactions. Unusually, the 12Y-2 complementarity-determining region 3 also adopts an extended beta-hairpin structure, suggesting a distinct selective advantage in accessing cryptic antigenic epitopes.

MeSH terms

  • Animals
  • Antibodies / chemistry*
  • Antibodies / genetics
  • Cell Adhesion Molecules / chemistry
  • Crystallography, X-Ray
  • Dimerization
  • Evolution, Molecular*
  • Immunoglobulin Variable Region / chemistry*
  • Immunoglobulin Variable Region / genetics
  • Models, Molecular
  • Molecular Conformation
  • Protein Structure, Quaternary*
  • Protein Subunits / chemistry
  • Protein Subunits / genetics
  • Receptors, Antigen / chemistry*
  • Receptors, Antigen / genetics
  • Receptors, Antigen, T-Cell / chemistry
  • Sharks / immunology*

Substances

  • Antibodies
  • Cell Adhesion Molecules
  • Immunoglobulin Variable Region
  • Protein Subunits
  • Receptors, Antigen
  • Receptors, Antigen, T-Cell

Associated data

  • PDB/1VER
  • PDB/1VES