1VER

Structure of New Antigen Receptor variable domain from sharks

Summary for 1VER

• Entry DOI: 10.2210/pdb1ver/pdb
• Related: 1VES
• Descriptor: New Antigen Receptor variable domain (2 entities in total)
• Functional Keywords: ig vnar, native, 12y-1, immune system
• Biological source: Orectolobus maculatus (spotted wobbegong)
• Total number of polymer chains: 1
• Total formula weight: 12266.76

Authors

Streltsov, V.A. (deposition date: 2004-04-05, release date: 2004-08-24, Last modification date: 2023-12-27)

Primary citation

Streltsov, V.A.,Varghese, J.N.,Carmichael, J.A.,Irving, R.A.,Hudson, P.J.,Nuttall, S.D.
Structural evidence for evolution of shark Ig new antigen receptor variable domain antibodies from a cell-surface receptor
Proc.Natl.Acad.Sci.USA, 101:12444-12449, 2004

PubMed 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.

PubMed: 15304650
DOI: 10.1073/pnas.0403509101

Experimental method

X-RAY DIFFRACTION (2.82 Å)