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. 2017 Mar 1;114(11):E2106–E2115. doi: 10.1073/pnas.1612444114

Fig. 3.

Fig. 3.

IFIT1 mRNA cap-binding mechanism. (A) The IFIT1 PPP (blue) adopts an extended conformation compared with the “bent” IFIT5 PPP (pink). The γ-phosphate from PPP–RNA-bound IFIT1 points toward the nearby unoccupied cap-binding pocket. (B) Protein cross-section and close-up the cap-binding pocket. This view is rotated by ∼180° compared with Fig. 2C. (C) Simulated annealing 2Fo–Fc omit map of the m7Gppp-moiety contoured at 1σ. Syn- and anti-configuration carbons are colored light blue and salmon, respectively. (D) Surface/stick representation of residues (colored by subdomain) abutting the m7G base moiety from above and below. The interplanar distance between m7G and Trp-147 is 3.4–3.7 Å. (E and F) Cartoon/stick representation of residues interacting with the m7Gppp-moiety. See also Movie S1. Shown are both conformations of the m7GpppA dinucleotide, which was modeled as a single residue during model building and refinement. (G) Cross-sections of the IFIT1 and IFIT5 RNA-binding tunnels (gray/black) with m7Gppp- or PPP-RNA (red sticks). The asterisk (*) shows where K48 and Q41 block the IFIT5 putative cap-binding pocket (Fig. S3 H–K).