The envelope glycoprotein (E) of West Nile virus (WNV) undergoes a conformational rearrangement triggered by low pH that results in a class II fusion event required for viral entry. Herein we present the 3.0-Å crystal structure of the ectodomain of WNV E, which reveals insights into the flavivirus life cycle. We found that WNV E adopts a three-domain architecture that is shared by the E proteins from dengue and tick-borne encephalitis viruses and forms a rod-shaped configuration similar to that observed in immature flavivirus particles. Interestingly, the single N-linked glycosylation site on WNV E is displaced by a novel ␣-helix, which could potentially alter lectin-mediated attachment. The localization of histidines within the hinge regions of E implicates these residues in pH-induced conformational transitions. Most strikingly, the WNV E ectodomain crystallized as a monomer, in contrast to other flavivirus E proteins, which have crystallized as antiparallel dimers. WNV E assembles in a crystalline lattice of perpendicular molecules, with the fusion loop of one E protein buried in a hydrophobic pocket at the DI-DIII interface of another. Dimeric E proteins pack their fusion loops into analogous pockets at the dimer interface. We speculate that E proteins could pivot around the fusion loop-pocket junction, allowing virion conformational transitions while minimizing fusion loop exposure.
West Nile virus (WNV), a member of the Flavivirus genus, is closely related to several arthropod-borne human pathogens, including Japanese encephalitis virus, St. Louis encephalitis virus, Yellow fever virus, Dengue virus (DENV), and Tick-borne encephalitis virus (TBEV). Endemic to parts of Africa, Asia, Europe, and the Middle East, WNV has recently spread to the Western Hemisphere (38). The virus cycles enzootically between birds and mosquitoes but can infect mammals, including humans. Most human infections are asymptomatic or mild, but in a small subset of individuals the infection develops into a severe neuroinvasive disease (18). Treatment for WNV infection is supportive, as there is currently no vaccine or specific therapy for use in humans (15).The WNV genome encodes 10 proteins, including three structural (capsid, premembrane [prM], and envelope [E]) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. These are translated as a single polypeptide, which is subsequently cleaved by viral and cellular proteases (6). The initial step toward virion generation occurs when the 11-kb positive-strand RNA genome, in complex with capsid protein, buds through the endoplasmic reticulum membrane. A lipid envelope coats the nascent flavivirus particles and contains 180 molecules each of E and prM organized into 60 asymmetric trimeric spikes consisting of prM-E heterodimers (45,46). At the apices of the spikes, prM caps the fusion loop of E (34), presumably to prevent premature fusion as the virus passes through the acidic secretory pathway (19). A furin-catalyzed membrane-proximal cleavage releases the Nterminal...