Fig. 4.

Accommodation of helical imperfections in the ternary complexes of pAgo proteins. Structural features of the duplexes formed in the seed region in ternary complexes of TtAgo⁷¹ (upper raw) and RsAgo⁵¹ (bottom) containing bulges or mismatches (shown in red) in the guide or target strand, in comparison with fully double-stranded duplex (“ds”). Only the part of the duplex between the guide 5′-end and the active site in the PIWI domain is shown (guide positions 1 through 10–12 for various complexes); Mg²⁺ ions bound in the MID-pocket (5′Mg²⁺) and in the active site (acMg²⁺) are indicated; some complexes of TtAgo were obtained with a catalytically inactive mutant and thus lack catalytic metal ions. The distortions of the double-helix are shown with red arrowheads; the nucleotide bulges can be either stacked-in (bulges in the guide strand; g-4-A-5 and g-7-T-8 in TtAgo) or flipped-out of the duplex (bulges in the target strand; t-6′-A-7′, t-9′-U-10′ for TtAgo, t-3′-AA-4′ for RsAgo). The ternary complexes were obtained with g-DNA/t-DNA or g-DNA/t-RNA for TtAgo, or g-RNA/t-DNA for RsAgo, as indicated. The PDB accession numbers are (from left to right): TtAgo, 4NCB, 5XP8, 5XOU, 5XOW, 5XPA; RsAgo, 6D8P, 6D8A, 6D92, 6D9L, 6D9K. See Supplementary Table 1 and Supplementary Fig. 3 for full description of each complex