Fig. 4: Cryo-EM structure of SARS-CoV-2 Omicron BA.1 Spike with ZCB11 Fab bound.

a Cryo-EM density map of spike trimer in complex with ZCB11 Fab. Two of three different states (3 u and 2u1d) are shown. Spike trimer is color-coded in green and Fab is in pink and purple in two states, respectively. Down RBD is color-coded in yellow. b Cryo-EM density map of RBD-Fab complex shown in two different views. Fab is color-coded in purple and RBD is in green. c Interaction between ZCB11 Fab and RBD. ZCB11 is shown as heavy chain (pink) and light chain (blue). Two interfaces are zoomed to show key residues responsible for the interaction. Hydrogen bonds and salt bridges are indicated as blue and yellow dashed lines, respectively. Key contact residues are also indicated. d Binding pattern of ZCB11 (purple) is compared with that of B1-182.1 (green, PDB: 7MLZ) or S2E12 (violet, PDB: 7K45). Sequence alignment shows the CDR H3 region including the unique RTI motif (underlined) in ZCB11. The red star highlights the S108 residue. e Sequence alignment of RBMs from different SARS-CoV-2 VOCs. Mutations and key residues are marked with numbers. Conserved key interface residues and mutant residues are labeled with blue and red stars, respectively. EM electron microscope, Fab antibody-binding fragment, RBD receptor-binding domain, CDR complementarity-determining region, RBM receptor-binding motif, VOCs variants of concern.