5F9F

Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA

Summary for 5F9F

• Entry DOI: 10.2210/pdb5f9f/pdb
• Related: 5F98 5F9H
• Descriptor: Probable ATP-dependent RNA helicase DDX58, RNA (5'-R(*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3'), ZINC ION, ... (7 entities in total)
• Functional Keywords: complex, rig-i, capped rna, self versus non-self, innate immunity, hydrolase-rna complex, hydrolase/rna
• Biological source: Homo sapiens (Human); More
• Cellular location: Cytoplasm: O95786
• Total number of polymer chains: 12
• Total formula weight: 525575.78

Authors

Wang, C.,Marcotrigiano, J.,Miller, M.T.,Jiang, F. (deposition date: 2015-12-09, release date: 2016-01-13, Last modification date: 2023-09-27)

Primary citation

Devarkar, S.C.,Wang, C.,Miller, M.T.,Ramanathan, A.,Jiang, F.,Khan, A.G.,Patel, S.S.,Marcotrigiano, J.
Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I.
Proc.Natl.Acad.Sci.USA, 113:596-601, 2016

PubMed Abstract: RNAs with 5'-triphosphate (ppp) are detected in the cytoplasm principally by the innate immune receptor Retinoic Acid Inducible Gene-I (RIG-I), whose activation triggers a Type I IFN response. It is thought that self RNAs like mRNAs are not recognized by RIG-I because 5'ppp is capped by the addition of a 7-methyl guanosine (m7G) (Cap-0) and a 2'-O-methyl (2'-OMe) group to the 5'-end nucleotide ribose (Cap-1). Here we provide structural and mechanistic basis for exact roles of capping and 2'-O-methylation in evading RIG-I recognition. Surprisingly, Cap-0 and 5'ppp double-stranded (ds) RNAs bind to RIG-I with nearly identical Kd values and activate RIG-I's ATPase and cellular signaling response to similar extents. On the other hand, Cap-0 and 5'ppp single-stranded RNAs did not bind RIG-I and are signaling inactive. Three crystal structures of RIG-I complexes with dsRNAs bearing 5'OH, 5'ppp, and Cap-0 show that RIG-I can accommodate the m7G cap in a cavity created through conformational changes in the helicase-motif IVa without perturbing the ppp interactions. In contrast, Cap-1 modifications abrogate RIG-I signaling through a mechanism involving the H830 residue, which we show is crucial for discriminating between Cap-0 and Cap-1 RNAs. Furthermore, m7G capping works synergistically with 2'-O-methylation to weaken RNA affinity by 200-fold and lower ATPase activity. Interestingly, a single H830A mutation restores both high-affinity binding and signaling activity with 2'-O-methylated dsRNAs. Our work provides new structural insights into the mechanisms of host and viral immune evasion from RIG-I, explaining the complexity of cap structures over evolution.

PubMed: 26733676
DOI: 10.1073/pnas.1515152113

Experimental method

X-RAY DIFFRACTION (2.601 Å)