Figure 5.

Structural and Functional Constraints of the COVA1-16 Epitope

(A) Location of the COVA1-16 epitope (yellow) on the SARS-CoV-2 S trimer when all three RBDs are in the down conformation (PDB: 6VXX; Walls et al., 2020). RBDs are represented as a white surface, N-terminal domains (NTDs) as a gray surface, and the S2 domain in a cartoon representation. Top panel: for visualization of the COVA1-16 epitope, the RBD and NTD from one of the three protomers was removed. Bottom panel: top and bottom views of the COVA1-16 epitopes on the three RBDs in the down conformation.

(B) The COVA1-16 epitope is shown in yellow on a ribbon representation of a SARS-CoV-2 S trimer (PDB: 6VXX; Walls et al., 2020). Epitope residues in the RBD involved in interaction with the S2 domain are shown as yellow sticks and S2 domain-interacting residues as dark gray sticks. Dashed lines indicate H-bonds. Interface residues were calculated using PISA software (Krissinel and Henrick, 2007). The S1 segment from the third protomer is omitted to clarify the view of the interfaces the COVA1-16 epitope makes with the S2 domain.

See also Figure S5.