Fig. 5: One-RBD-up conformation of Omicron spike impairs the binding and neutralizing potencies of S304 antibody. | Nature Communications

Fig. 5: One-RBD-up conformation of Omicron spike impairs the binding and neutralizing potencies of S304 antibody.

From: Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape

Fig. 5

a Detailed interactions between Omicron RBD (pink) and S304 Fab (blue and purple). Yellow and red dashed lines represent hydrogen bonds and salt bridges, respectively. b Interaction analysis between prototypic RBD (tan) and S304 Fab (blue and purple) in the RBD-S304-S309-S2H14 complex (PDB: 7JX3)24. Yellow and red dashed lines represent hydrogen bonds and salt bridges, respectively. c Comparison of key residues of the epitope targeted by S304 in the prototype (tan) (PDB: 7JX3)24 and Omicron (pink). Key residues shared by the prototype and Omicron are labeled in purple, otherwise are labeled with their respective colors. Mutations of the Omicron RBD are shown as spheres. d Superimposition of the S304-bound Omicron RBD (purple) on the apo spike trimer of Omicron. Three protomers of which are colored corresponding to Fig. 1b. The star shape represents the clash site. e Superimposition of the S304-bound Omicron RBD on the ACE2-bound spike trimer of Omicron with two-RBD-up conformation revealed that the steric clash between S304 and the neighboring RBD and NTD remained. f The atomic structure of three S304-bound spike trimer of the SARS-CoV-2 prototype (PDB: 7JW0)24. g Superimposition of the model in f on the two ACE2-bound Omicron spike.

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