Fig. 4: Structurally informed phylogenetics.
From: Mapping glycoprotein structure reveals Flaviviridae evolutionary history
a, Left, 3Di-based E structural phylogeny. The scale bar indicates the number of 3Di character substitutions per site (see Methods for details of tree selection). Right, representative structures superposed using flexible FATCAT49 with a ColabFold model of West Nile virus E protein as reference (green). Structures are colour-coded as in the phylogeny. The protein alignments provide structurally aligned consensus-level amino acid sequences for the fusion loop, domain III and transmembrane domain. Conserved residues are highlighted. b, Left, combined 3Di and amino acid-based E1 structural phylogeny. The scale bar indicates the number of 3Di and amino acid character substitutions per site. Right, representative structures are superposed with Hepacivirus F E1 protein. Alignments demonstrate consensus-level homology in the E1 helical hairpin and transmembrane domain. Structures are colour-coded as in the phylogeny. c, Left, combined 3Di and amino acid-based structural phylogeny of E2 protein. Right, representative structures are superposed with Hepacivirus F E2. Consensus-level homology in E2 back layer, stem and transmembrane domain are provided. The basal Wenling moray eel Hepacivirus is marked in both the E1 and E2 trees. AA, amino acid.
