1JRH

COMPLEX (ANTIBODY/ANTIGEN)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Neutralizing epitopes on the extracellular interferon gamma receptor (IFNgammaR) alpha-chain characterized by homolog scanning mutagenesis and X-ray crystal structure of the A6 fab-IFNgammaR1-108 complex.

Sogabe, S.Stuart, F.Henke, C.Bridges, A.Williams, G.Birch, A.Winkler, F.K.Robinson, J.A.

(1997) J Mol Biol 273: 882-897

  • DOI: 10.1006/jmbi.1997.1336
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The extracellular interferon gamma receptor alpha-chain comprises two immunoglobulin-like domains, each with fibronectin type-III topology, which are responsible for binding interferon gamma at the cell surface. The epitopes on the human receptor rec ...

    The extracellular interferon gamma receptor alpha-chain comprises two immunoglobulin-like domains, each with fibronectin type-III topology, which are responsible for binding interferon gamma at the cell surface. The epitopes on the human receptor recognized by three neutralizing antibodies, A6, gammaR38 and gammaR99, have been mapped by homolog scanning mutagenesis. In this way, a loop connecting beta-strands C and C' in the N-terminal domain was identified as a key component of the epitopes bound by A6 and gammaR38, whereas gammaR99 binds to the C-terminal domain in a region including strands A and B and part of the large C'E loop. The epitope for A6 was confirmed in a crystal structure of a complex between a recombinant N-terminal receptor domain and the Fab fragment from A6, determined by X-ray diffraction to 2.8 A resolution. The antibody-antigen interface buries 1662 A2 of protein surface, including 22 antibody residues from five complementarity determining regions, primarily through interactions with the CC' surface loop of the receptor. The floor of the antigen binding cavity is formed mainly by residues from CDR L3 and CDR H3 while a surrounding ridge is formed by residues from all other CDRs except L2. Many potential polar interactions, as well as 13 aromatic side-chains, four in VL, six in VH and three in the receptor, are situated at the interface. The surface of the receptor contacted by A6 overlaps to a large extent with that contacted by interferon-gamma, in the ligand-receptor complex. However, the conformation of this epitope is very different in the two complexes, demonstrating that conformational mobility in a surface loop on this cytokine receptor permits steric and electrostatic complementarity to two quite differently shaped binding sites.


    Related Citations: 
    • Dissection of the Extracellular Human Interferon Gamma Receptor Alpha-Chain Into Two Immunoglobulin-Like Domains. Production in an Escherichia Coli Thioredoxin Gene Fusion Expression System and Recognition by Neutralizing Antibodies
      Williams, G., Ruegg, N., Birch, A., Weber, C., Hofstadter, K., Robinson, J.A., Aguet, M., Garotta, G., Schlatter, D., Huber, W.
      (1995) Biochemistry 34: 1787
    • Variable Region Cdna Sequences and Characterization of Murine Anti-Human Interferon Gamma Receptor Monoclonal Antibodies that Inhibit Receptor Binding by Interferon Gamma
      Bridges, A., Birch, A., Williams, G., Aguet, M., Schlatter, D., Huber, W., Garotta, G., Robinson, J.A.
      (1995) Mol Immunol 32: 1329

    Organizational Affiliation

    Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY A6
L
213Mus musculusMutation(s): 0 
Gene Names: Igkc
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY A6
H
219Mus musculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
INTERFERON-GAMMA RECEPTOR ALPHA CHAIN
I
108Homo sapiensMutation(s): 1 
Gene Names: CDNAIFNGR1
Find proteins for P15260 (Homo sapiens)
Go to UniProtKB:  P15260
NIH Common Fund Data Resources
PHAROS  P15260
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.74α = 90
b = 90.8β = 90
c = 101.58γ = 90
Software Package:
Software NamePurpose
MARXDSdata collection
X-PLORmodel building
X-PLORrefinement
MARXDSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-03-25
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance