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Figure 2.
Figure 2: Comparison of structural details between the binary
Ago complex with bound guide DNA and the ternary complex with
added target RNA. a, Expanded view of the ternary complex
highlighting the guide DNA (1–10)-target RNA (1'–9') duplex
and Mg^2+-coordinated catalytic residues (D478, D546 and D660)
of the RNase H fold of the PIWI domain. Intermolecular hydrogen
bonds between the Ago protein and the DNA guide strand in red
are shown by dashed lines. b, Positioning of the sugar-phosphate
backbone of the target RNA strand spanning the
mismatch-containing 10–11-step relative to the catalytic
residues of the PIWI domain. c, Comparison of the trajectory of
traceable bound guide DNA in the binary (bases 1–11 and
18–21 in silver) and ternary (bases 1–10 and 19–21 in red)
Ago complexes after superposition of their 5'-phosphate-binding
pockets. d, Superposition of the guide DNA (red)-target RNA
(blue) duplex spanning the 2–8 seed segment on A-form (left
panel) and B-form (right panel) helices (silver) after best-fit
superposition of the target RNA strand of the ternary Ago
complex with one strand of the A/B-form helices. e, Positioning
of stacked residues 6–10 of the DNA guide strand relative to
R548, with emphasis on intermolecular interactions involving the
sugar-phosphate backbone. f, Relative positioning of the 6 to
10/11 segment of the bound guide DNA strand and R548 in the
binary (guide strand in silver, protein in cyan) and ternary
(guide strand in red, protein in magenta) Ago complexes. The
conformational change in the protein on proceeding from binary
to ternary Ago complexes is indicated by a red arrow.
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