Extended Data Fig. 6: Structural details of the interactions between Crt-SPARTA and nucleic acids.

a, The nucleic acid substrates of Crt-SPARTA form an unusual B-form duplex. The structure of Crt-SPATA–RNA–DNA hybrid duplex (coloured green and yellow) is superimposed to an ideal B-form duplex (coloured grey, left) and an ideal A-form duplex (coloured grey, right) using the software Matchmaker. b, Magnified view of the nucleic-acid-binding pocket of Crt-SPARTA–RNA–DNA complex with superimposed TtAgo–DNA–DNA complex (PDB: 4N47). Guide RNA (green) of Crt-SPARTA superimposed with the guide DNA of TtAgo (black) are shown with ribbon models. The trigger ___domain (blue) is close to the guide RNA but there are no direct contacts between them. The superimposed guide DNA of TtAgo extends near the 5’-phosphate-binding pocket in Crt-PIWI, whereas the 5′ terminus of Crt-guide RNA is around five base steps behind. c, Target DNA (yellow) of Crt-SPARTA with superimposed template DNA of TtAgo (black); TtAgo template DNA extends around five base steps ahead of Crt-SPARTA template DNA. The trigger ___domain recognizes the 3′ terminus of Crt-SPARTA template DNA, whereas the 3′ terminus of the superimposed TtAgo DNA template strand is around five base steps ahead. d–g, Magnified views of the Crt-SPARTA–nucleic acid interactions. Residues and nucleotides participating in the interaction are shown as stick models and labelled. d, Nucleic acid recognition by the lasso unit. e, Nucleic acid recognition by the Crt-TIR-pPAZ ___domain. f, Nucleic acid recognition by the Crt-PIWI RNase H ___domain. g, Nucleic acid recognition by the Crt-PIWI-Box ___domain.