Fig. 3: Cryo-EM reconstruction of SINV/EEEV in complex with a potently neutralizing intact IgG.

A Cryo-EM reconstruction of SINV/EEEV particles in complex with EEEV-373 IgG was determined by single particle averaging with icosahedral symmetry to 4.6 Å resolution. The black triangle represents the asymmetric unit, with the symmetry axes depicted by the red pentagon (5-fold axis), triangle (3-fold axis), and circle (2-fold [i2] axis) symbols. The quasi-three-fold (q3) spikes are represented by the blue triangles. The scale bar (in Å) represents the radial distance from the center of the virus. B A close-up view of the i2 axis displays a single EEEV-373 IgG molecule diagonally spanning across the axis to connect two q3 spikes. The q3 and icosahedral three-fold (i3) spikes are labeled in dark blue text accordingly. In comparison to the SINV/EEEV particle density, the density of the IgG molecule is relatively weak, and to help elucidate the complex, the two arms of the IgG molecule are indicated by the dark blue dotted lines. C, D Localized reconstruction, focused classification, and refinement with C1 symmetry of the two q3 spikes cross-linked by the EEEV-373 IgG molecule were performed to improve the resolution of the reconstruction. A top (C) or side (D) view of the improved reconstruction from the i2 axis perspective are illustrated. The q3 spikes, constant and variable domains of EEEV-373 are indicated accordingly. The map is colored according to the coloring of the fitted model in ChimeraX. The grey regions fall slightly outside of the fitted model, while the relative protein domains of E1 (domain I: orange, domain II: light pink, domain III: light orange), E2 (domain A: cyan, domain B: teal, domain C: aqua, β-ribbon connector: purple), EEEV-373 heavy chain (green) and light chain (yellow) are colored accordingly. E, F Local resolution map of the volume as shown in C and D. E, F correspond to the viewing directions in C and D, respectively. The scale bar (in Å) represents the resolution gradient.