PDBsum entry 2d03

Immune system

PDB id: 2d03

Contents

Protein chains

217 a.a. *

212 a.a. *

Ligands

GOL ×7

MES

PEG

Waters ×303

* Residue conservation analysis

PDB id:

2d03

Name:

Immune system

Title:

Crystal structure of the g91s mutant of the nna7 fab

Structure:

Anti-glycophorin a type n immunoglobulin light chain. Chain: l. Synonym: fab nna7 light chain. Engineered: yes. Mutation: yes. Anti-glycophorin a type n immunoglobulin heavy chain. Chain: h. Synonym: fab nna7 heavy chain. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.97Å R-factor: 0.218 R-free: 0.262

Authors:

K.Xie,S.C.Song,S.L.Spitalnik,J.E.Wedekind

Key ref:

K.Xie et al. (2005). Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition. Acta Crystallogr D Biol Crystallogr, 61, 1386-1394. PubMed id: 16204891 DOI: 10.1107/S0907444905023851

Date:

23-Jul-05 Release date: 24-Jan-06

Protein chain

No UniProt id for this chain

Struc: 217 a.a.

Protein chain

No UniProt id for this chain

Struc: 212 a.a.

DOI no: 10.1107/S0907444905023851

Acta Crystallogr D Biol Crystallogr 61:1386-1394 (2005)

PubMed id: 16204891

Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition.

K.Xie, S.C.Song, S.L.Spitalnik, J.E.Wedekind.

ABSTRACT

The NNA7 Fab antibody fragment recognizes the human N-type blood-group antigen comprised of the N-terminal glycopeptide of glycophorin A (GPA). A mutant form of this Fab fragment, NNA7-G91S, exhibits markedly reduced antigen binding. To provide insight into how these Fab fragments recognize this glycopeptide antigen, the crystal structures of NNA7 and NNA7-G91S were solved and refined to 1.83 and 1.97 A resolution, respectively. Both molecules are composed of the same heavy (H) chain Fd fragment, but each contains a slightly different light (L) chain owing to the G91S substitution. Specifically, the G91S mutation pushes the backbone of the neighboring H chain away from complementarity-determining region 3 (CDR3) of the L-chain variable region, allowing an additional glycerol cryoprotectant molecule to enter the antigen-combining site near the putative location of O-linked glycosylation. Each Fab fragment also possesses a well defined 2-(N-morpholino)ethanesulfonic acid (MES) molecule trapped in its antigen-combining site, as well as a crystallographic symmetry-related molecule comprising an amino-acid sequence that is virtually identical to the N-terminus of GPA. The MES molecule interacts with the H-chain CDR in a manner reminiscent of antibody-carbohydrate complexes. These results suggest a model for recognition of the glycopeptide antigen that accounts for the deleterious effect of the G91S substitution.

Selected figure(s)

Figure 1.
Figure 1 Schematic depiction of the primary sequence of the antigenic GPA glycopeptide. (a) The polypeptide sequence of the N-terminus depicting the amino-acid polymorphisms that differentiate the M and N antigens. O-Glycosylated residues are marked with asterisks. (b) Structures of the O-glycans at positions 2, 3 and 4 that contribute to MN antigenicity. The sugars are abbreviated as follows: Gal, galactose; GalNAc, N-acetylgalactosamine; NANA, N-acetylneuraminic (sialic) acid.

Figure 6.
Figure 6 Superposition of the structures of the antigen-combining sites of NNA7 (yellow) and NNA7-G91S (blue). Differences in the structures are accentuated by changes in the label color.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1386-1394) copyright 2005.

Figures were selected by an automated process.