Fig. 2: Structures of R1-32 in complex with SARS-CoV-2 spike and R1-32 epitope. | Nature Microbiology

Fig. 2: Structures of R1-32 in complex with SARS-CoV-2 spike and R1-32 epitope.

From: SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope

Fig. 2

a, Cryo-EM densities (low-pass filtered to 10 Å) of S-GSAS/6P spikes bound to R1-32 Fab and ACE2 at different stoichiometries. R1-32 Fab, NTD, RBD and ACE2 are highlighted in magenta, blue, cyan and dark green, respectively; the rest of the spike is coloured grey. RBDs adopting ‘down’ positions are indicated. b, Structure of the 3:3:3 spike protomer:Fab:ACE2 complex derived from the boxed density in a. R1-32-H and R1-32-L are coloured in magenta and purple. Structure of the RBD:Fab:ACE2 portion is shown on the right panels. c, R1-32 HCDR2 and HCDR3 epitopes are shown with rotations in viewing angles. Residues interacting with R1-32-H and R1-32-L are coloured in cyan and green, respectively. Highly buried residues (buried surface area >70% of accessible surface area) are coloured blue to highlight the HCDR2 and HCDR3 epitopes. R1-32 HCDR2 interacts with epitopes by hydrophobic contacts (left panel). R1-32 HCDR3 primarily uses backbone carbonyl oxygens and amide nitrogens (indicated by red and cyan dots, respectively) to hydrogen bond with epitope (right panel). d, Left: surface representation of the R1-32 epitope, with surface areas coloured as in c. Right: epitope area within the orange outline is buried by NTD in an ‘RBD’ down spike protomer. e, Epitopes of R1-32 are coloured as in d and substituted residues in the Omicron BA.1 variant are highlighted in red.

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