Figure 1

Collinear arrangement of similar structures in BDV G and VSV G. The post fusion secondary structure of VSV G as solved and numbered by Roche and coworkers [30] is depicted with α-helices as cylinders and β-sheets as arrows. The α-helices predicted by PHD In BDV G are indicated similarly. β-sheets (t) and (u) of VSV G are not present in the protein data base structure (2cmz.pdb). In VSV G, α-helices predicted by PHD are indicated by dashed boxes and predicted β-sheets are identified with dashed arrows. Amino acids are numbered beginning after the putative signal sequences enclosed in parentheses. Plum amino acids: N-glycosylation sites. Sequences with significant WWIHS scores in the fusion domain (II) were identified by MPeX and colored red. Hydrophobic transmembrane domains (violet) were predicted using TMpred. A class III domain nomenclature is used here that can apply to both class II and III VFP: domain I (green), domain II (yellow), domain III (blue), and stem domain (indigo). This unified nomenclature assigns domain II (IV in the VSV G nomenclature of Roche et al. [30], I in the HSV-1 gB nomenclature of Heldwein et al. [32] and Ia and Ib in the baculovirus nomenclature of Kadlec et al. [34]) as the class III fusion domain as in class II VFPs. In addition to minor adjustments in the ends of domains, the current class III VFP numbering also combines two interacting domains into domain III (I + II in Roche's VSV G nomenclature, III + IV in Heldwein's HSV-1 gB nomenclature and Kadlec's baculovirus nomenclature). The domain numbering originally proposed is also indicated. UA represents "hinge" aa not assigned to domains in VSV G in the prior scheme.