Extended Data Fig. 3: Mapping of the mutations present in Omicron to the spike’s surface.

a. The spike shown in top (left panel) and in side view (middle and right panels). The spike trimer is shown in surface representation with the three protomers coloured in light grey, light blue and light green. N-terminal and the receptor-binding (NTD and RBD) domains are labelled for the protomer in green only. The represented spike (PDB: 6XR8) is in the closed conformation, i.e., with all three RBDs in the “Down” conformation⁴⁴. The RBD surface of interaction with hACE2 (which is partially occluded in a closed spike) is coloured in yellow. The amino acid differences in the spike of the Omicron variant with respect to the initial Wuhan sequence are marked in red. In the right panel, the front subunit was removed to show changes in S2 and in the C-terminal segment of S1 (labelled) that map to the trimer interface, which could impact the stability of the spike trimer. b. The RBD view down the hACE2 binding surface (left panel) and in two other orthogonal orientations (middle and right panel), as indicated. The hACE2 binding surface is coloured in yellow and the residues altered in Omicron are in red. The RBD surfaces that are buried and exposed in a closed spike are coloured in light cyan and white, respectively. The ovals outline the location of the epitopes of neutralizing antibodies of the various classes that have been described¹⁷.