Zika virus M protein latches and locks the E protein from transitioning to an immature state after prM cleavage

During flavivirus maturation, the structural proteins prM (pre-membrane) and E (envelope) undergo extensive low pH-mediated conformational changes, transitioning from spiky trimeric to smooth dimeric prM/E heterodimers which allow for furin cleavage of prM into pr and M and forms the irreversible mature conformation of smooth M/E heterodimers. The mechanisms of irreversible conformational changes to E protein following the pr cleavage are not understood. Utilizing cryo-EM structures of immature virus and structure-based mutagenesis of Zika virus, we identified two critical “latching and locking” interactions mediated by M protein residues Arg38 and Trp19, respectively, that stabilize the E protein structure in the smooth mature stage. M protein thus latches and locks the E protein in an irreversible mature structure, preventing premature fusion in the secretory pathway. Our studies provide mechanistic insights into the reversible structural transition of immature trimeric spikes and the irreversible transition of smooth dimeric M/E heterodimers critical for virus infectivity.