Fig. 2: RT synthesizes a DNA ‘harpoon’ that stabilizes the complex.
From: Structural basis of antiphage defence by an ATPase-associated reverse transcriptase
a The ncRNA sequence of retron I-A from E. coli is mapped onto the covariance model shown in Fig. 1c. Conserved stem-loop motifs (SL-1, SL-2, and SL-3), the clamp (CL) and termination sequence (TS) are highlighted. b AlphaFold3-predicted structure of the ncRNA-RT complex highlight features of the ncRNA identified in (a). c The ncRNA-RT structure prediction reveals that the RT thumb domain is trapped between SL-1 and SL-3, while SL-3 is positioned between the thumb and palm domains of the RT. The magnified region highlights the conserved VTG motif, which is predicted to make contacts with the DNA backbone, positioning the priming guanosine (G8, yellow) and adenosine 7 (A7, purple) near the active site (YADD, pink). d Like the predicted structure of ncRNA-RT prior to msDNA synthesis (panel c), the experimentally determined structure of retron I-A reveals interactions between the RT thumb domain and SL-1. The duplex formed by the TS and the 3′ end of the msDNA is positioned between the thumb and palm domains, occupying the site previously occupied by SL-3 in panel c. The magnified region highlights the 3′ end of the cDNA contacting the YADD active site. e The IS1 flexible loop of the SMC ATPase contains a series of basic residues that interact with the msDNA ‘harpoon’. f The RT makes extensive interaction with one of ATPases (cyan). g–i Coiled-coil domains in IS2 of the ATPase form distinct structural features on either side of the complex. g On one side, the coiled-coil domains from opposing ATPases bear hug the DNA harpoon. i On the opposite side, the IS2 coiled-coils form dorsal fin-like feature.
