a, Detailed view of the primer (blue)-template (yellow) duplex and partially extruded priming loop (grey) in the mixed-initiation state. Close packed bases of -5U, A8 and A10 butt against residues 652–655 (grey sticks) of the repositioned priming loop and a salt-bridge between conserved PB1 Asp655 and PB2 Arg218 (red sticks). b, Superposition of priming loop conformations as seen in the two pre-initiation state (grey, cryoEM and cyan, PDB entry 5MSG), mixed-initiation state (green) and elongation state (orange). The left view is orientated as in Fig. 2 and the right view is vertically rotated by 50°. c, Fit of the priming loop residues PB1/631-661 into the cryoEM density of the pre-initiation state filtered at 3.16 Å resolution. d, Fit of the priming loop residues PB1/631-661 into Fo-Fc omit electron density map of the 15-mer capped primer mixed-initiation state crystal structure contoured at 3 σ. e, Fit of the priming loop residues PB1/631-661 into the cryoEM density of the elongation state filtered at 3.20 Å resolution.