Fig. 6. Conformational changes between pre-initiation and elongation-mimicking states.

a LACV-L FL in pre-initiation state. Left panel: cryo-EM map colored as in Fig. 1. Middle panel: close-up view. Right panel: close-up view rotated 90° compared to the middle panel. For more clarity, only the lid, thumb ring, and mid domains are shown in the middle and right panels and are colored in light blue, blue, and beige. The mid-thumb ring linker (1741–1751) is shown in purple gray. The priming loop is shown in dark blue. All these elements are labeled. The lid domain is closed and the residue Y1696 from the α-helix 70 points towards the cavity. The priming loop is disordered between residues 1410 and 1423 (dotted line). Priming loop movement occurring during elongation is depicted with a dark blue arrow. b LACV-L FL in elongation-mimicking state. Equivalent panels as in a are shown with domains and loops colored as in a. The mid-thumb ring linker contains residues 1741–1761 at elongation. The template tunnel entry and exit, the product exit are shown. The lid domain is open and Y1696 from the α-helix 70 interacts with the product-mimicking RNA. The priming loop is ordered and interacts with the lid, the thumb ring, and the mid-thumb ring linker. c Superimposition of the thumb and thumb ring (shown in transparent gray) in pre-initiation and elongation-mimicking state of LACV-L FL. The bridge, the lid, and the priming loop in pre-initiation are shown in red. The bridge, the lid and the priming loop in elongation-mimicking state are shown in purple, light blue and dark blue. Their rotation between the two states is labeled. Movement of the priming loop between the two states is shown with an arrow. d Priming loop and mid-thumb ring linker at pre-initiation (left) and elongation (right). Numbering of both elements are indicated. Residues from the lid and thumb ring that interact with the priming loop at pre-initiation and/or elongation are shown. The 8 Å displacement between the mid-thumb ring linker extremity at pre-initiation and elongation is indicated with an arrow.