Tick-borne encephalitis virus (TBEV) causes 13,000 cases of human meningitis and encephalitis annually. However, the structure of the TBEV virion and its interactions with antibodies are unknown. Here, we present cryo-EM structures of the native TBEV virion and its complex with Fab fragments of neutralizing antibody 19/1786. Flavivirus genome delivery depends on membrane fusion that is triggered at low pH. The virion structure indicates that the repulsive interactions of histidine side chains, which become protonated at low pH, may contribute to the disruption of heterotetramers of the TBEV envelope and membrane proteins and induce detachment of the envelope protein ectodomains from the virus membrane. The Fab fragments bind to 120 out of the 180 envelope glycoproteins of the TBEV virion. Unlike most of the previously studied flavivirus-neutralizing antibodies, the Fab fragments do not lock the E-proteins in the native-like arrangement, but interfere with the process of virusinduced membrane fusion.

We report on a conformational transition of dengue virus when changing the temperature from that present in its mosquito vectors to that of its human host. Using cryoelectron microscopy, we show that although the virus has a smooth surface, a diameter of ∼500 Å, and little exposed membrane at room temperature, the virions have a bumpy appearance with a diameter of ∼550 Å and some exposed membrane at 37°C. The bumpy structure at 37°C was found to be similar to the previously predicted structure of an intermediate between the smooth mature and fusogenic forms. As humans have a body temperature of 37°C, the bumpy form of the virus would be the form present in humans. Thus, optimal dengue virus vaccines should induce antibodies that preferentially recognize epitopes exposed on the bumpy form of the virus.host temperature | irreversible and conformational change | temperature dependence | cryo-EM D engue virus (DENV), together with other significant arthropod-borne human pathogens such as West Nile, yellow fever, and Japanese encephalitis viruses, belongs to the flavivirus genus of the Flaviviridae family of RNA viruses (1, 2). The Flavivirus genus has been subdivided into the mosquito-borne viruses (e.g., dengue, yellow fever, and Japanese encephalitis), the tick-borne viruses, and those that do not use arthropod vectors (3). The four related DENV serotypes are transmitted by the Aedes aegypti and Aedes albopictus mosquitoes. The absence of a coordinated and comprehensive mosquito abatement programs has contributed to the global spread of the mosquito vectors and human DENV infection. DENV now infects ∼230 million people worldwide each year, with an estimated 3.6 billion people living in areas of risk (4). DENV infection can cause dengue fever, more severe dengue hemorrhagic fever (DHF), and life-threatening dengue shock syndrome (DSS) (5). Secondary infection with a heterologous DENV serotype increases the risk of developing DHF and DSS. Currently, there are neither licensed vaccines nor effective antiviral drugs against DENV. Indeed, new approaches to vaccine development may be needed, as the most advanced tetravalent live-attenuated DENV vaccine candidate showed a poor 30% overall efficacy rate in a recently published phase 2b clinical trial (6, 7).DENV has an 11-kb, positive-sense RNA genome that encodes a capsid protein, a precursor membrane glycoprotein, an enveloped glycoprotein (E), and seven nonstructural proteins (8). The X-ray crystallographic structure of the E protein (9-11) shows that it has three ectodomains (DI, DII, and DIII). Domain DII has a fusion loop at its distal tip and DIII has an Ig-like fold. The E ectodomain is anchored to the viral membrane by its C-terminal transmembrane region and its ∼50 amino acids amphipathic α-helical "stem" region (9,(12)(13)(14).The structure of mature DENV, propagated at ∼30°C, determined by combining cryoelectron microscopy (cryo-EM) of the whole virus (8, 15) with crystallography of the protein components (9-11, 16) shows 90 E dimers arranged in an icosahedral...

Enterovirus 71 is a picornavirus associated with fatal neurological illness in infants and young children. Here we report the crystal structure of enterovirus 71 and show that, unlike in other enteroviruses, the “pocket factor”, a small molecule that stabilizes the virus, is partly exposed on the floor of the canyon. Thus the structure of antiviral compounds may require a hydrophilic head group designed to interact with residues at the entrance of the pocket.

Many pleomorphic, lipid-enveloped viruses encode matrix proteins that direct their assembly and budding, but the mechanism of this process is unclear. We have combined X-ray crystallography and cryoelectron tomography to show that the matrix protein of Newcastle disease virus, a paramyxovirus and relative of measles virus, forms dimers that assemble into pseudotetrameric arrays that generate the membrane curvature necessary for virus budding. We show that the glycoproteins are anchored in the gaps between the matrix proteins and that the helical nucleocapsids are associated in register with the matrix arrays. About 90% of virions lack matrix arrays, suggesting that, in agreement with previous biological observations, the matrix protein needs to dissociate from the viral membrane during maturation, as is required for fusion and release of the nucleocapsid into the host's cytoplasm. Structure and sequence conservation imply that other paramyxovirus matrix proteins function similarly.