Fig. 4: C04 binds to the distal end of 229E RBD and neutralizes 229E PsV after affinity maturation.
From: Antigenic mapping reveals sites of vulnerability on α-HCoV spike protein
a Crystal structure of Fab C04 in complex with 229E RBD in cartoon representations. The heavy and light chain of C04 are colored dark green and wheat respectively, while 229E RBD are colored gray. The binding site of host receptor hAPN is depicted with blue spheres. b Contact residues are colored orange (heavy chain) and blue (light chain) on surface representation of 229E RBD. CDR loops engaging 229E RBD are shown and labeled. c The heavy (dark green) and light chain (wheat) of C04 and the RBD (gray) are shown as surface representations. CDRH3 (magenta) is depicted in cartoon to illustrate its neat fitting into the surface pocket on 229E RBD. d Structural superimposition of free C04 (purple), RBD-bound C04 (wheat) and RBD-bound S11(blue) illustrating the conformational change of CDRH3 upon binding RBD. All structures are shown as cartoon representations and the inset is the close-up view of CDRH3 region. e Left: The epitope of C04 appears buried in all-RBD-down conformation but becomes fully exposed in one-RBD-up conformation. Right: Binding of Fab C04 would slightly interfere with the binding of hAPN to neighboring ‘up’ protomer (colored pink, anti-clockwise). Structure of Fab C04-bound 229E S trimer was modeled by superimposing the structure of RBD-C04 onto the one-RBD-up 229E S trimer. Next, this structure was aligned with hAPN-229E RBD complex based on the 229E RBD in ‘up’ position. f Binding affinities of parental C04 and affinity-matured antibodies against 229E S trimer or RBD were characterized by SPR. Of the affinity-matured antibodies, antibody S11 (blue) and S15 (red) exhibited up to 11-fold increase in their affinity for 229E S trimer and RBD. g Neutralization profiles for IgG S11 (blue), S15 (red) and R10 (orange) are compared to that of parental IgG C04 (black) against 229E PsV. Individual data points are shown as filled blue circles (S11), red diamonds (S15), orange triangles (R10) and black triangles (C04) respectively.
