The slicer catalytic site and a role for the N-domain as a duplex wedge. (A) Assembly of the slicer site. The figure show zoomed-in views of the slicer catalytic site, in the binary  and 19 mer ternary  complexes. The figure illustrates conformational changes that accompany complementary target strand annealing. Key residues are highlighted. The guide is omitted in the right panel for clarity. The 19 mer ternary complex structure shown was obtained using an N478 catalytic site mutant  and, therefore, the structure is partially-distorted with only a single catalytic magnesium ion. (B) The N-domain as a duplex wedge. Two views of the 19 mer ternary complex  illustrating encapsulation by TtAgo of the fully annealed complementary guide/target duplex and blockage at position 16 by the N-domain (orange). The view on the left shows the duplex from the guide 5' end and the widened nucleic acid binding channel between the MID/PIWI lobe (pale green) and PAZ (dark green). The view on the right shows the same structure rotated and from above, illustrating enclosure of the duplex and the abrupt arrest at position 16 (guide)/16' (target). Nucleotides 17-21 of the guide and 17'-19' of the target are invisible, presumably disordered, though it is assumed they bypass either side of the N-domain.
Parker Silence 2010 1:3 doi:10.1186/1758-907X-1-3