Fig. 9: AlphaFold predictions of a complex between NS3h and 5BSL3 (A–D) and of a putative NS3h–NS5B–RNA priming complex (E–G) for synthesis of the (−) strand.

A Predicted aligned error (PAE) plot for a complex between the helicase domain NS3h and the cis-acting element of the (+) strand, 5BSL3. Colour code is from red (large PAE) to blue (low PAE, i.e., pairs of residues in correct relative positions). Note that the low PAE values between NS3h and the 5BSL3 cluster in two pairs of streaks correspond to 5BSL3.1 and 5BSL3.3. B This prediction is displayed in cartoon representation, with NS3h coloured magenta (domain 1), pink (D2) and dark pink (D3), and 5BSL3 in rainbow colours from blue (5’ end) to red (3’ end). D3 is labelled in italics on all structural panels. D1467 is displayed as spheres and labelled. A cif file containing the AF3 prediction is included in the Supplementary Data 3. C The same complex where NS3h is depicted as an electrostatic surface. D Zoom in on the Phe-loop. F1468, D1467, and D1471 are displayed as spheres and labelled. E PAE plot of the best prediction obtained for a complex between the helicase domain NS3h, the polymerase NS5B and the 3’-end of the (+) strand HCV RNA, here a variant of stem-loop 1 (SL1’). F This NS3h–NS5B–SL1’ complex displayed as in B, with NS5B blue and SL1’ in rainbow colours. For the latter, extra bases have been added and are depicted in grey to picture how the 3’ end of the (+) strand would come out of NS3h and are connected by the dotted grey line to the template-binding groove of NS5B. For comparison of this model to the recently published structures of dengue virus complexes, see Supplementary Fig. 8. The parallel dotted black lines denote the membrane in which NS3 is anchored through its interaction with NS4A and NS5B through its transmembrane C-terminal helix. A cif file containing the AF3 prediction is included in the Supplementary Data 3. G The same complex as in F seen from the other side with NS3h and NS5B depicted as electrostatic surfaces.