1T6V

Crystal structure analysis of the nurse shark new antigen receptor (NAR) variable domain in complex with lysozyme

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structure of a shark single-domain antibody V region in complex with lysozyme.

Stanfield, R.L., Dooley, H., Flajnik, M.F., Wilson, I.A.

(2004) Science 305: 1770-1773

  • DOI: 10.1126/science.1101148
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Cartilaginous fish are the phylogenetically oldest living organisms known to possess components of the vertebrate adaptive immune system. Key to their immune response are heavy-chain, homodimeric immunoglobulins called new antigen receptors (IgNARs), ...

    Cartilaginous fish are the phylogenetically oldest living organisms known to possess components of the vertebrate adaptive immune system. Key to their immune response are heavy-chain, homodimeric immunoglobulins called new antigen receptors (IgNARs), in which the variable (V) domains recognize antigens with only a single immunoglobulin domain, akin to camelid heavy-chain V domains. The 1.45 angstrom resolution crystal structure of the type I IgNAR V domain in complex with hen egg-white lysozyme (HEL) reveals a minimal antigen-binding domain that contains only two of the three conventional complementarity-determining regions but still binds HEL with nanomolar affinity by means of a binding interface comparable in size to conventional antibodies.

    Organizational Affiliation: 

    Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
L, M
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
novel antigen receptor
N, O
113Ginglymostoma cirratum
Find proteins for Q8AXI4 (Ginglymostoma cirratum)
Go to UniProtKB:  Q8AXI4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download SDF File 
Download CCD File 
N, O
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 75.790α = 90.00
b = 113.810β = 90.00
c = 58.440γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
EPMRphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance