1VER

Structure of New Antigen Receptor variable domain from sharks


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

Streltsov, V.A.Varghese, J.N.Carmichael, J.A.Irving, R.A.Hudson, P.J.Nuttall, S.D.

(2004) Proc Natl Acad Sci U S A 101: 12444-12449

  • DOI: 10.1073/pnas.0403509101
  • Primary Citation of Related Structures:  
    1VES, 1VER

  • 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 top ...

    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.


    Organizational Affiliation

    Division of Health Sciences and Nutrition, Commonwealth Scientific and Industrial Research Organization, and Cooperative Research Centre for Diagnostics, 343 Royal Parade, Parkville 3052, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
New Antigen Receptor variable domainA111Orectolobus maculatusMutation(s): 0 
Find proteins for Q6X1E7 (Orectolobus maculatus)
Explore Q6X1E7 
Go to UniProtKB:  Q6X1E7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.170 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.259α = 90
b = 97.259β = 90
c = 65.228γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2004-04-05 
  • Released Date: 2004-08-24 
  • Deposition Author(s): Streltsov, V.A.

Revision History 

  • Version 1.0: 2004-08-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance