Extended Data Fig. 6: Structural basis of 2H2 antibody retaining neutralization potency and 8D3/S5D2/3C1 antibodies losing their neutralization potency against Omicron.
From: Molecular basis of receptor binding and antibody neutralization of Omicron
a, Model of the Omicron RBD-2H2 Fab interaction interface, obtained by docking of the RBD-bound 2H2 (PDB ID: 7DK4) onto the RBD-1 structure from our current Omicron S-open. b, The electrostatic surface properties of Omicron and WT RBDs, with the black line depicting the footprint of 2H2 on RBD-1. The residues with substantial electrical charge changes are indicated. c, The electrostatic surface property of 2H2 Fab, with the black line depicting the footprint of RBD-1 on 2H2. d–f, Docking of RBD-bound 8D3/S5D2/3C1 (PDB ID: 7W9F/7WCR/7DCC, respectively) onto the Omicron RBD-1 structure. Residue S477N that may potentially clash with the 8D3 Fab is labeled (d). Residues S477N and T478K that may break the H-bond network between RBD and S5D2 Fab are labeled (e). Residue S375F that may contribute to the Omicron’s escape of 3C1 binding and neutralization is labeled (f). All substituted residues in Omicron RBD-1 are colored in red.
