2D03

Crystal structure of the G91S mutant of the NNA7 Fab

Summary for 2D03

• Entry DOI: 10.2210/pdb2d03/pdb
• Related: 1T2Q
• Descriptor: anti-glycophorin A type N immunoglobulin light chain, anti-glycophorin A type N immunoglobulin heavy chain, GLYCEROL, ... (6 entities in total)
• Functional Keywords: antibody, immune system
• Biological source: Mus musculus (house mouse); More
• Total number of polymer chains: 2
• Total formula weight: 48607.02

Authors

Xie, K.,Song, S.C.,Spitalnik, S.L.,Wedekind, J.E. (deposition date: 2005-07-23, release date: 2006-01-24, Last modification date: 2024-11-13)

Primary citation

Xie, K.,Song, S.C.,Spitalnik, S.L.,Wedekind, J.E.
Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition.
Acta Crystallogr.,Sect.D, 61:1386-1394, 2005

PubMed 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.

PubMed: 16204891
DOI: 10.1107/S0907444905023851

Experimental method

X-RAY DIFFRACTION (1.97 Å)