Fig. S6.
RNA binding mechanism at N1-N4. (A) Interactions between IFIT1 and RNA at N1/N2 and (B) at N3/N4. The protein is oriented such that we are looking along the RNA-binding tunnel from the 3′-exit (similar orientation as Fig. S2C). Note that K336 and the backbone carbonyl of G190 are H-bonded to N2 and N4, respectively. Concerning Fig. 8 and the multiple roles of R187, Y157, H289, and Q290: R187 packs against the ribose of N1, coordinates Y218 and Y157 (Fig. S3G), and interacts with m7G and bridging PPP (Fig. 3 E and F); Y157 contacts the N1 ribose and N1 adenine through van der Waals; Q290 is H-bonded to the 3′ oxygen of N2 and the internucleotide phosphate between N2 and N3; H289 is H-bonded to the 2′-OH of N2, and contacts the ribose of N3 via van der Waals. V372 could potentially clash with methylation at the N6 position of the first adenosine (see Discussion). (C) Simulated annealing 2Fo–Fc omit map of N1/N2 contoured at 1σ. Two views rotated by 180° are shown. The dinucleotide conformation here resembles that found in CpG dinucleotides of Z-form RNA and UUCG tetraloop sequences (39). The defining feature of this rare dinucleotide motif is the antiparallel arrangement of the two riboses (with their respective O4′ atoms pointing toward each other), and a lone pair–π stack between the O4′ atom of N1 and the base of N2. (D) Simulated annealing 2Fo–Fc omit map of N3/N4 contoured at 1σ. N3/N4 adopt standard A-form helical geometry. (E) Hydrogen-bonds between the RNA bases and the waters (red spheres) inside the tunnel. N6 methylation of the first adenosine could disrupt water mediated interactions at the first nucleotide (see Discussion). (F) N1 and N2 adopt C2′-endo and C3′-endo conformations respectively. RNA nucleotides are typically in equilibrium between the two, but generally favor the C3′-endo conformation.