Fig. 4: Cryo-EM structures of CVA16 in complex with 9B5 Fab.

Cryo-EM maps of CVA16–9B5 in three distinct states, C1 (a), C2 (b), and C3 (c). The density maps are viewed along the two-fold axis. The color bar indicates the radius from the center of the particle (unit in Å). The black triangle indicates one icosahedral asymmetric unit. Density maps of the two-fold related protomers of the C1 (d), C2 (e), and C3 (f) conformers, superimposed with fitted models. 9B5 Fab was removed for clarity. VP1, VP2, VP3, and VP4 are colored in blue, green, red, and yellow, respectively; the same color scheme is used throughout. The black pentagon, ellipse, and triangle represent the five-fold, two-fold, and three-fold axes, respectively. The major differences among the conformers are indicated by yellow dashed rectangles. Central sections of the C1 (g), C2 (h), and C3 (i) density maps. j Zoomed-in view of the CVA16–9B5 C1 interaction interface, demonstrating that most side chain densities were well resolved. k Binding interface between CVA16 protomer and 9B5 Fab. VH and VL of 9B5 are colored in cyan and hotpink, respectively. The five-fold axis is also shown. l Zoomed-in views of the interactions between VP1 loops of CVA16 and the CDR and framework (FR) regions of 9B5. Black dashed lines indicate hydrogen bonds, and red springs indicate salt bridges. m Roadmap indicating the footprints of 9B5 on the CVA16 virion surface, obtained by RIVEM. Viral residues are colored by radius. VL and VH are indicated by white and yellow contour lines, respectively. The potential SCARB2-binding region is shown in orange contour lines. The positively charged viral residues (K141, R166, K241, K242, and H245) that bind heparan sulfate and the residues (T97, T100, and T103) mutated in 9B5 escape variants are indicated with black and cyan contour lines, respectively. n The structure of EV71–SCARB2 complex (PDB: 6I2K) was fitted into the CVA16 two adjacent protomers (P1 in khaki and P2 in gray), revealing that SCARB2 (orange) would clash with 9B5 Fab (blue) that is bound to the adjacent protomer.