5F9F: Crystal Structure Of Rig-i Helicase-rd In Complex With 24-mer Blunt- End Hairpin Rna

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.
PDB ID: 5F9FDownload
MMDB ID: 135543
PDB Deposition Date: 2015/12/9
Updated in MMDB: 2016/01
Experimental Method:
x-ray diffraction
Resolution: 2.6  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 5F9F: dodecameric; determined by author and by software (PISA)
Molecular Components in 5F9F
Label Count Molecule
Proteins (6 molecules)
Probable Atp-dependent RNA Helicase Ddx58(Gene symbol: DDX58)
Molecule annotation
Nucleotide(1 molecule)
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')
Molecule annotation
Chemicals (29 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB