The Structural Basis of 5′ Triphosphate Double-Stranded RNA Recognition by RIG-I C-Terminal Domain

• Published in: Structure (London) Vol. 18; no. 8; pp. 1032 - 1043
• Main Authors: Lu, Cheng, Xu, Hengyu, Ranjith-Kumar, C.T., Brooks, Monica T., Hou, Tim Y., Hu, Fuqu, Herr, Andrew B., Strong, Roland K., Kao, C. Cheng, Li, Pingwei
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 11-08-2010
• Subjects: Base Sequence; Chromatography, Gel; Crystallography, X-Ray; DEAD Box Protein 58; DEAD-box RNA Helicases - chemistry; DEAD-box RNA Helicases - genetics; DEAD-box RNA Helicases - metabolism; Electrophoretic Mobility Shift Assay; Escherichia coli; Humans; Models, Molecular; Molecular Sequence Data; Mutagenesis; Polyphosphates - metabolism; Protein Binding; Protein Conformation; Receptors, Immunologic; RNA; RNA, Double-Stranded - chemistry; RNA, Double-Stranded - metabolism; Sequence Analysis, DNA; Surface Plasmon Resonance; Ultracentrifugation; RNA
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2010.05.007

RIG-I is a cytosolic sensor of viral RNA that plays crucial roles in the induction of type I interferons. The C-terminal domain (CTD) of RIG-I is responsible for the recognition of viral RNA with 5′ triphosphate (ppp). However, the mechanism of viral RNA recognition by RIG-I is still not fully understood. Here, we show that RIG-I CTD binds 5′ ppp dsRNA or ssRNA, as well as blunt-ended dsRNA, and exhibits the highest affinity for 5′ ppp dsRNA. Crystal structures of RIG-I CTD bound to 5′ ppp dsRNA with GC- and AU-rich sequences revealed that RIG-I recognizes the termini of the dsRNA and interacts with the 5′ ppp through extensive electrostatic interactions. Mutagenesis and RNA-binding studies demonstrated that similar binding surfaces are involved in the recognition of different forms of RNA. Mutations of key residues at the RNA-binding surface affected RIG-I signaling in cells.
► RIG-I CTD binds 5′ triphosphate dsRNA with high affinity ► Structures of RIG-I CTD bound to 5′ triphosphate dsRNA with GC- and AU-rich sequences ► RIG-I and LGP2 CTD bind dsRNA with or without triphosphate differently ► Overlapping sets of residues are involved in binding of various forms of RNA