Structural and functional insights into 5′-ppp RNA pattern recognition by the innate immune receptor RIG-I

The innate immune system relies on a series of specific receptors that recognize RNAs that might come from viruses. The structure of the C terminal domain of one such receptor, RIG-I, in complex with 5'ppp-dsRNA, now indicates the basis of recognition of the observable 5'pp-RNA, through interactions that are shown to be needed for tight binding and a cellular response to this trigger. RIG-I is a cytosolic helicase that senses 5′-ppp RNA contained in negative-strand RNA viruses and triggers innate antiviral immune responses. Calorimetric binding studies established that the RIG-I C-terminal regulatory domain (CTD) binds to blunt-end double-stranded 5′-ppp RNA a factor of 17 more tightly than to its single-stranded counterpart. Here we report on the crystal structure of RIG-I CTD bound to both blunt ends of a self-complementary 5′-ppp dsRNA 12-mer, with interactions involving 5′-pp clearly visible in the complex. The structure, supported by mutation studies, defines how a lysine-rich basic cleft within the RIG-I CTD sequesters the observable 5′-pp of the bound RNA, with a stacked phenylalanine capping the terminal base pair. Key intermolecular interactions observed in the crystalline state are retained in the complex of 5′-ppp dsRNA 24-mer and full-length RIG-I under in vivo conditions, as evaluated from the impact of binding pocket RIG-I mutations and 2′-OCH 3 RNA modifications on the interferon response.