Fig. 6: Potential binding modes of EEEV-373 IgG at the icosahedral 2-fold axis of SINV/EEEV particles.

A Preferred binding mode orientation of EEEV-373 IgG across the icosahedral 2-fold (i2) axis (q3.1-q3.3). A cartoon representation of the fitted atomic models of the E2 protein (cyan) and EEEV-373 IgG (heavy chain: green, light chain: yellow) at the i2 axis (blue circle) is shown. The E1 protein is omitted for clarity. The four q3 spikes (q3.1-q3.4) and the two i3 spikes (i3.1-i3.2) are labeled in bolded text accordingly. The distance (in Å) between the Cα atoms of the last residue (Lys222; red spheres) on strain G of the constant domains (CH1) of the two Fab arms of EEEV-373 (42.5 Å) is indicated by the dotted line. B In addition to the observed binding mode, there are five alternative ways (C–G) EEEV-373 could cross-link viral spikes across the i2 axis as depicted. The distance (in Å) between the Cα atoms of the last residue (Lys222; red spheres) on strain G of the constant domains (CH1) of the two Fab arms of EEEV-373 are indicated by the dotted lines (C [i3.1-i3.2]: 64.0 Å; E [q3.1-q3.4]: 41.0 Å; F [q3.1-i3.2]: 48.9 Å; G [q3.3-q3.4]: 44.2 Å). For the i3.1-q3.1 (D) or q3.3-q3.4 (G) binding modes, steric clashes are observed between the light chain constant domains of EEEV-373 (yellow) as indicated by the black dotted circle (D) or the black box (G). E For the q3.1-q3.4 binding mode, movement of the constant domains as indicated by the purple arrows may lead to steric clashes. F For the q3.1-i3.2 binding mode, EEEV-373 may also bind in this orientation. However, a 60° rotation of one Fab arm with respect to the other Fab arm may reduce the likelihood of binding. The distance and steric hindrance constraints observed in C–G likely contribute to the observation of EEEV-373 in the preferred binding mode orientation (A) with binding of the two Fab arms to the q3.1 and q3.3 spikes across the i2 axis.