Fig. 7: Schematic diagram of conformational changes in Lassa virus L protein associated with promoter binding and RNA synthesis activity.

a On the surface of the inactive/resting L protein core, there is mutually exclusive positioning (black double-arrow) of either the α-bundle and pendant (APO-RIBBON structure) or the EN domain (APO-ENDO, 3END-ENDO structures). When placed on the core, the inhibitory peptide (cyan) autoinhibits the EN domain by binding in its active site. In the absence of the 5′ vRNA, the 3′ vRNA binds preferentially, base-specifically, into a distinct secondary 3′ RNA binding site between the pyramid and thumb domains (3END-ENDO/CORE structures). b Upon full promoter binding, major conformational changes occur (based on PRE-INITIATION, DISTAL-PROMOTER, MID-LINK structures). The 5′ end nucleotides 0–9 are bound in a hook-like conformation in a specific pocket outside the active site. The distal promoter (formed by 3′ and 5′ vRNA nucleotides 12–19) is positioned by tight association with the α-bundle and pendant, with concomitant rotation of the pyramid domain. This forces release of the 3′ vRNA from the secondary binding site, allowing it to be directed towards the RNA synthesis active site (marked by the white A in the teal circle). Positioning of the pendant domain next to the distal promoter displaces the EN domain, which relocates to the other end of the L protein core with the inhibitory peptide contacting its surface leaving the EN active site accessible. In this configuration, the EN is presumed to be in close vicinity to the CBD-like domain and could potentially cleave an incoming capped RNA to generate a transcription primer by ‘cap-snatching’. How the capped primer associates with the CBD-like domain and how it is navigated towards the active site to initiate transcription remains elusive. c Upon transition to the elongation state, the distal promoter duplex melts and the pendant domain is released, which allows the pyramid to rotate back and re-establish the availability of the secondary 3′ end binding site (ELONGATION structure). We presume the 3′ vRNA template, after exiting the active site, wraps around the L protein core and rebinds to the secondary 3′ end binding site, as described for influenza virus polymerase complex¹⁸. The EN repositions once again and together with the mid-link and CBD-like domains form a highly structured ring around the putative product exit channel. The EN active site is again autoinhibited, this time by the relocation of its C-terminal helix (181–188) to the active site.