1SQ2

Crystal Structure Analysis of the Nurse Shark New Antigen Receptor (NAR) Variable Domain in Complex With Lysozyme

• PDB DOI: https://doi.org/10.2210/pdb1SQ2/pdb

• Classification: HYDROLASE/IMMUNE SYSTEM
• Organism(s): Gallus gallus, Ginglymostoma cirratum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-03-17 Released: 2004-08-24 
• Deposition Author(s): Stanfield, R.L., Dooley, H., Flajnik, M.F., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.225 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Starting Models: experimental

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

• PubMed: 15319492 
• DOI: https://doi.org/10.1126/science.1101148
• Primary Citation of Related Structures:  
  1SQ2, 1T6V


• 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), 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.73 kDa 
• Atom Count: 2,045 
• Modelled Residue Count: 241 
• Deposited Residue Count: 242 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A [auth L]	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
novel antigen receptor	B [auth N]	113	Ginglymostoma cirratum	Mutation(s): 0
UniProt
Find proteins for Q8AXI4 (Ginglymostoma cirratum) Explore Q8AXI4  Go to UniProtKB:  Q8AXI4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth L], E [auth L], F [auth L], G [auth L], H [auth N]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.225 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.02	α = 90
b = 109.84	β = 90
c = 29.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-24 
Deposition Author(s): Stanfield, R.L., Dooley, H., Flajnik, M.F., Wilson, I.A.

Revision History  

• Version 1.0: 2004-08-24
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary