PDBsum entry 1jrh

Complex (antibody/antigen)

PDB id: 1jrh

Contents

Protein chains

167 a.a. *

180 a.a. *

95 a.a. *

Waters ×30

* Residue conservation analysis

PDB id:

1jrh

Name:

Complex (antibody/antigen)

Title:

Complex (antibody/antigen)

Structure:

Antibody a6. Chain: l. Fragment: fab fragment.Pepsin digestion of intact antibody. Antibody a6. Chain: h. Fragment: fab fragment.Pepsin digestion of intact antibody. Interferon-gamma receptor alpha chain. Chain: i. Fragment: n-terminal domain.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Homo sapiens. Human. Organism_taxid: 9606. Gene: cdna. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

2.80Å R-factor: 0.246 R-free: 0.314

Authors:

F.K.Winkler,S.Sogabe

Key ref:

S.Sogabe et al. (1997). 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. J Mol Biol, 273, 882-897. PubMed id: 9367779 DOI: 10.1006/jmbi.1997.1336

Date:

23-Sep-97 Release date: 25-Mar-98

Protein chain

P01837  (IGKC_MOUSE) -  Immunoglobulin kappa constant from Mus musculus

Seq: 107 a.a.

Struc: 167 a.a.

Protein chain

P01869  (IGH1M_MOUSE) -  Ig gamma-1 chain C region, membrane-bound form from Mus musculus

Seq: 393 a.a.

Struc: 180 a.a.*

Protein chain

P15260  (INGR1_HUMAN) -  Interferon gamma receptor 1 from Homo sapiens

Seq: 489 a.a.

Struc: 95 a.a.*

* PDB and UniProt seqs differ at 24 residue positions (black crosses)

DOI no: 10.1006/jmbi.1997.1336

J Mol Biol 273:882-897 (1997)

PubMed id: 9367779

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.

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

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 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.

Selected figure(s)

Figure 3.
Figure 3. The epitopes recognized by A6 and gR38 (in red) and gR99 (in blue) on a ribbon representation of the IFNg.IFNgR complex as determined by le Du et al. (unpublished results). IFNg (2 < 17 kDa) is shown in pink and green, the IFNgR in white (N-terminal domain D1) and yellow (C-terminal domain D2) (see Figure 1). The red and blue regions are those where changes are introduced in mutant 6 (CC loop) and 8 (EF loop) (red), and 13 (strand A), 14 (strand B) and 21 (C E loop) (blue) (see Table 1).

Figure 8.
Figure 8. Residues at the A6. IFNgR interface; on the receptor (bottom left, grey and turquoise), and on A6 (top right) CDR L1 (light blue), L2 (dark blue), L3 (green), CDR H1 (yellow), H2 (orange) and H3 (red) (orientation as in Figure 5). Figure was pro- duced using MOLMOL (Koradi et al., 1996).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 273, 882-897) copyright 1997.

Figures were selected by an automated process.