Fig. 4: Cryo-EM analyses on the Omicron S–S3H3 Fab complex.
From: Molecular basis of receptor binding and antibody neutralization of Omicron
a, b, Side and top views of the cryo-EM map of the Omicron S-open–S3H3 (a) and S-close–S3H3 complex (b), with the heavy chain (HC) and light chain (LC) of S3H3 Fab in medium blue and violet red, respectively. This colour scheme is followed throughout this figure. c, Conformational comparison between Omicron S-open–S3H3 (light green) and Omicron S-open (orange), indicating a slight twist of the RBDs of S-open–S3H3 and the downward rotations of RBD-1 (up to 9.1º) and SD1. d, Model map fitting of the focus-refined Omicron SD1–S3H3 structure, and the zoomed-in view of the Omicron SD1–S3H3 interaction interface. The side chain densities at the interface were well resolved. e, The S3H3 binding on SD1 of protomer 2. f, The structural elements involved in the interaction between S3H3 Fab and SD1 are labelled. The SD1 T547K substitution is also shown in red. The residues of SD1 in proximity to S3H3 (less than 4 Å) are indicated and coloured in transparent orange (related to Extended Data Table 4). g, The SD1–S3H3 interaction interface analysed using PISA, with the major involved structural elements labelled (the spring represents the salt bridge, and the black dashed line represents the hydrogen bond).
