Extended Data Fig. 6: Details and VOC comparisons for Cryo-EM structure of neutralizing antibody 2130-1-0114-112 in complex with Omicron BA.2 RBD.
From: Computationally restoring the potency of a clinical antibody against Omicron
a, RBD residues within 7 Å of 2130-1-0114-112. RBD shown in red, with BA.2 mutated residues in orange, and 2130-1-0114-112 in yellow/green. b, CDRH3 Glu112 and RBD Lys440, shown with the EM map and distance between the side chains. c, d, 3D representation of the interaction plot between RBD and 2130-1-0114-112 HC (c, yellow) and LC (d, green). 2130-1-0114-112 is shown as stick and RBD as gray spheres with the contact residues in red. Contact residues are labelled and numbered. e, Fab COV-2130 paratope and epitope residues involved in hydrogen bonding (dashed lines; distances in Å) and hydrophobic interactions with WA1/2020 RBD; compare with Fig. 6d showing BA.2/2130-1-0114-112 interactions. Residues forming hydrophobic interactions are shown as curved lines with rays. Atoms are shown as circles, with oxygen, carbon, and nitrogen in red, black, and blue respectively. Image created with Ligplot + . f, Atomic model of the RBD-Fab complex superimposed with WA1-RBD (light brown PDB: 7L7E), XBB1.1-RBD (pink PDB: 8IOS), and BQ1.1 (gray PDB 8IF2). BA.2 RBD is shown in red, with BA.2 mutations in orange. 2130-1-0114-112 HC and LC are yellow and green, with mutations in cyan and blue. Hydrogen bonds are shown as dashed lines.
