Flaviviruses are small, highly organized enveloped viruses with a spherical shape [4, 11] . They contain a positive-sense RNA genome packaged by the viral capsid protein. The nucleocapsid is surrounded by a lipid bilayer containing the viral membrane protein E. Flaviviruses infect cells by receptor engagement at the plasma membrane, endocytic uptake, and a membrane fusion reaction triggered by the low pH of the endosome compartment [12, 13] . The viral E protein binds the receptor and drives the fusion of the viral and endosome membranes to initiate virus infection. The pre-fusion structure of the E protein ectodomain (here referred to as E9) shows that E contains three domains composed primarily of b-sheets: a central domain I (DI) connecting on one side to the elongated domain II (DII) with the hydrophobic fusion loop at its tip, and connecting via a flexible linker on the other side to the immunoglobulin-like domain III (DIII) [14, 15, 16, 17, 18, 19] (Figs. 1A, S1). Although these regions are not present in the truncated E9 ectodomain, DIII connects to a stem domain and C-terminal membrane anchor (TM). The E protein in mature infectious flavivirus is organized in homodimers that lie tangential to the virus membrane [20] . Within each dimer the E proteins interact in a head to tail fashion, with the fusion loop of each E protein hidden in a hydrophobic pocket formed by DI and DIII of the dimeric E partner.