Fig. 1

Structural features of targetable elements (fusion peptide, stem helix, and heptad repeats 1 and 2) in SARS-CoV-2 S2 subunit. a Schematic structure of SARS-CoV-2 spike protein. The conserved glycosylation sites within the SARS-CoV-2 S2 subunit are shown and marked as ψ. b Conformational transition of SARS-CoV-2 S2 subunit from pre- (PDB: 6XR8) to post-fusion (PDB: 7E9T) state. c The electrostatic surface representation of the FP binding area and the structural illustration of the FP in pre-fusion spike (PDB: 6XR8). The segment corresponding to FP is shown in sticks and colored in cyan. d The stem 3-helix bundle is shown in pre-S trimer (PDB: 6XR8). The detailed residues are shown in sticks and colored in green. e The electrostatic surface representation of the SH binding area and structural illustration of SH in post-fusion spike (PDB: 6XRA). The segment corresponding to SH is shown in sticks and colored in green. f–h Structure of the SARS-CoV-2 six-helix bundle (6-HB) in the post-fusion conformation (PDB: 6LXT). The symmetry-related structure of the 6-HB bundle is shown. Structures from a top view (up) and a side view (down) are presented in (f). The electrostatic surface of the HR2 binding site is shown in (g). The detailed hydrophobic and hydrogen-bond interactions between HR1 and HR2 are shown and labeled in (h). The distance cut-off is 3.1 Å for hydrogen-bond contact