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. 2022 Oct 17;17(10):e0276241. doi: 10.1371/journal.pone.0276241

Fig 1. S, N, and M peptide subpools and their relationship to each protein structure.

Fig 1

The structures of the S glycoprotein, and N and M proteins and their individual domains are aligned with the peptide subpools for each protein. Since constituent 15mer peptides partially overlap, each subpool also partially overlaps adjoining subpools. Consensus amino acid positions are shown in each protein. Some differences are reported, for example the S heptad repeat is variously reported to end at amino acid 1211 (reference #19), and 1213 (reference #20). Spike S glycoprotein (reference #20): Signal peptide (S); N-terminal domain (NTD); RBD (receptor-binding domain); SD1/SD2 (subdomain 1 and 2); 1 (fusion peptide); 2 (HR1, heptad repeat); 3 (central helix); CD (connector domain); 4 (HR2, heptad repeat); 5 (transmembrane domain); 6 (cytoplasmic tail); the S1/S2 and S2’ cleavage sites (reference #23). S protein subpools predominantly aligned with S domains: Sp1, Sp2 NTD; Sp3 NTD/RBD; Sp4 RBD; Sp5 SD1/SD2; Sp6 SD1/SD2 including S1/S2 cleavage site; Sp7 fusion peptide; Sp8 heptad repeat; Sp9 central helix/connector domain; Sp10 heptad repeat/transmembrane domain/cytoplasmic tail. Nucleocapsid protein N (reference #24): domain N1; domain N2 (N-terminal domain [NTD] or RNA binding domain); domain N3 (contains a serine-arginine rich region); domain N4 (C-terminal domain [CTD]; domain N5. N protein subpools predominantly aligned with N domains: Np1 domains N1 and part of N2; Np2 domains N2 and N3; Np3 domains N3 and N4; Np4 domains N4 and N5. Membrane protein M (reference #26): N (NTD, N-terminal domain); I, II and III (transmembrane domains); C (CTD, C-terminal domain). M protein subpools predominantly aligned with M domains: Mp1 NTD, 1, II and III; Mp2 CTD.