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. 2021 Dec 2;12:7018. doi: 10.1038/s41467-021-27305-5

Fig. 2. L protein in the pre-initiation state.

Fig. 2

a Ribbon diagram of the PRE-INITIATION structure with pendant domain (pink), α-bundle (dark blue), pyramid (teal), 3′ vRNA nts 7–19 (orange) and 5′ vRNA nts 0–19 (pink) highlighted in colour and indicated by name. b Interactions of the L protein pyramid (teal), pendant (pink) thumb-ring (yellow) and thumb (green) domains with the 3′ vRNA are shown. Important amino acid side chains and the RNA nucleotides of 3′ and 5′ vRNA are shown as sticks with respective labels. c Viral RNA observed in this structure with a 5′ vRNA hook structure composed of 5′ vRNA nts 0–9 and a distal duplex region involving 5′ vRNA nts 12–19 and 3′ vRNA nts 12–19. The 3′ vRNA nts 1–11 are directed towards the RdRp active site (towards AS) but not resolved. d Close-up of the 5′ RNA hook binding site involving the fingers domain (blue), finger node (light yellow), pyramid base (wheat) and helical region (raspberry). Residues important for the RNA-protein interface and nucleotides are shown as sticks and are labelled. e Schematic presentation of the promoter RNA (3′ vRNA in orange, 5′ vRNA in pink) in the PRE-INITIATION structure. Nucleotides 1–6 of the 3′ vRNA, which are not resolved, are coloured in grey. Distal duplex and 5′ hook regions are labelled.