Fig. 2: Structural characterization of monoclonal antibody 8-9D.

a Surface rendered representations and ribbon diagrams showing the structure of the Omicron BA.5 spike in complex with three 8-9D Fabs. Only the variable region of 8-9D Fab is displayed in the ribbon diagrams (right). The “up” RBDs are in orange, the heavy chain of 8-9D is colored pink, and the light chain is colored blue. The selected region in the dashed square shows one RBD with one bound Fab. b Ribbon diagrams showing the RBD interacting with the variable region of the 8-9D Fab (left). The rendered surface of 8-9D Fab and RBD in an open-up view (right). The epitopes on the RBD recognized by the 8-9D heavy chain and light chain are colored pink and blue, respectively. The ribbons of 8-9D Fab and RBD are colored the same as in (a). The ACE2 footprint on RBD is highlighted with green lines. c Ribbon diagrams showing the comparisons of the binding orientations of ACE2 and 8-9D on the RBD. The 8-9D Fab and RBD are colored the same as in (a) and ACE2 is colored green. The green, pink, and orange balls are the centroids of ACE2, 8-9D Fab, and RBD, respectively. d Detailed ribbon and stick diagrams showing the hydrogen bonds between the RBD and complementarity-determining region (CDR) of 8-9D heavy and light chains. RBD, 8-9D heavy and light chains are colored the same as in (a). Residues involved in hydrogen bond formation are shown in sticks with oxygen and nitrogen atoms colored red and blue, respectively. e Ribbon and stick diagrams comparing the corresponding residues in Omicron BA.5 RBD (in a solid rectangle) and in the wild-type RBD (in a dashed rectangle). The residues and hydrogen bonds in wild type RBD are colored green. The complex structure of 8-9D and the wild-type RBD was obtained through structural modeling with COOT⁷⁰ and Foldit Standalone⁷⁴. RBD, 8-9D heavy and light chains are colored the same as in (a).