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Many flaviviruses require NS5A protein for the encapsidation of their genomes. Binding of NS5A to incoming virions can induce structural changes in the polyprotein precursor that allow the host cell protease NS3 to cleave the polyprotein, releasing the viral RNA genome into the host cell. We have used site-directed mutagenesis to investigate the structure of the NS5A-NS3 protease binding site. Our results showed that mutations located in the amino acid sequence immediately preceding the NS3 protease cleavage site produced a similar decrease in the sensitivity of virions to arboviral NS3 proteases. These changes were mapped to the NS5A-NS3 binding site by both competition and structural studies. The marked decrease in sensitivity of mutant viral RNAs to NS3 protease correlates with the formation of a stably structured RNA species that is not susceptible to premature maturation, and which contains a novel amino acid sequence on the carboxy-terminal side of the NS3 site. These results are consistent with the hypothesis that the NS3-cleavage site
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