Fig. 4

Cryo-EM structures of the spike protein S and RBD complexed with CR9 Fab. a Side view and top view of surface representations of the structures of SARS-CoV-2 BA.5 S trimer in complex with Fab CR9 (three up RBDs) with different colors for each S monomer (green, light purple, cyan) and Fab CR9 (light chain: pink; heavy chain: blue). b Side views of the binding surface representations of the structures of SARS-CoV-2 BA.5 RBD in complex with Fab CR9. c Surface representations of the SARS-CoV-2 BA.5 RBD in complex with Fab CR9 and hACE2(yellow), The hACE2 is presented as surface with 70% transparency. The color scheme is the same as in (a). d Cartoon representation of the interacting residues in RBD and CDRs in CR9. The residues (R403, N405, N417, D420, N487, Y489 and H505) comprising the epitope are shown as spheres and labeled. The CR9 Fab is presented as surface with 30% transparency and CDRs involved in the interaction with RBD are highlighted. e Details of the interactions between CR9 and SARS-CoV-2 BA.5 RBD. Residues involved in the formation of hydrogen bonds are shown as sticks and labeled. Hydrophobic patches are shown in gray surface representation. Hydrogen bonds are depicted as yellow dots. The color scheme is the same as in (a). f The footprint of CR9 Fabs shown on BA.5 RBD, the conserved sites in Omicron indicated in light salmon