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. 2024 Sep 24;52(19):11895–11910. doi: 10.1093/nar/gkae820

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© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site-for further information please contact journals.permissions@oup.com

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Figure 3. — The overall structures of KmAgo-DM_gDtD and KmAgo_gDtD. (A) Domain architecture of ternary complexes with amino acid numbering. Domains and their unstructured residues are colored and labeled. (B–E) Cryo-EM density map (Top) and ribbon diagrams (Bottom) of pre1-KmAgo-DM_gDtD (B), pre2-KmAgo_gDtD (C), cleaved-KmAgo_gDtD (D), released-KmAgo_gDtD (E). (Middle) The sequence and pairing of gDNA (blue) and tDNA (red) strands in the ternary complex. Nucleotides that were not modelled are represented in gray. The black triangle in (D) and (E) denotes the location of the cleavage site. (F) Superposition of pre1-KmAgo-DM_gDtD (colored as in B) and KmAgo_gDNA (gray). (G) Enlarged view of the interaction between position 9 and F253. The left panel is the binary structure, and the right panel is the pre1-KmAgo-DM_gDtD. (H) Significant conformational changes in the PAZ domain are indicated by red arrows.