Fig. 3
Crystal structure of antibody H3v-47 Fab in complex with H3N2v HA (A/Minnesota/11/2010) and identification of the epitope. a Overall structure of the H3v-47 Fab- H3N2v HA complex. One HA/Fab protomer of the trimeric complex is colored with HA1 in yellow, HA2 in orange, Fab heavy chain in green, and Fab light chain in cyan. N-linked glycans are depicted as colored balls representing their atom types (carbon in pink, oxygen in red and nitrogen in blue). The other two protomers are in gray, but the third Fab molecule is hidden behind the HA trimer. b Zoomed-in view of the interaction between H3N2v HA and H3v-47 Fab with color coding as in a. H3v-47 Fab binds to the region spanning the receptor-binding and vestigial esterase sub-domains (shown as a solid surface in yellow and wheat, respectively) mainly using CDRs H2, H3, L1, and L3. The contact regions ascribed to antigenic sites A and E are highlighted in orange or red, respectively. c H3v-47 epitope mapped onto the H3N2v HA surface. The footprint of antibody H3v-47 on the HA shows the central role of antigenic E site residues for H3v-47 binding. The interacting surface contributed by residues from antigenic sites A or E is colored in red or orange, respectively, whereas residues that contribute to the epitope outside of these two antigenic sites, are colored in yellow. d Antibody contact residues (sticks) that interact with the HA with CDRs H2, H3, L1, L3, and FR3 in the light chain. e Specific interactions (H-bonds, salt bridges, hydrophobic interactions, and VDW contacts) between H3v-47 and its footprint residues shown as sticks. The H-bonds and salt bridges are labeled using dash lines
