Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir

Figures

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  Fig. 1. Assembly of an active nsp12-nsp7-nsp8 RdRp complex and its inhibition by remdesivir. (A) Schematic diagram for the components of the RdRp complex, containing nsp12, nsp7, and nsp8. The polymerase motif (A to G) and the β hairpin specific to SARS-CoV-2 are highlighted. (B) Sequence of the RNA duplex with a 5′ U10 overhang as a template for primer extension and RdRp-RNA complex assembly. (C) The recombinant RdRp complex shows polymerase activity in vitro. The primer strand is labeled with fluorescence at the 5′ end. (D) Elongation of the partial RNA duplex by the purified RdRp complex and its inhibition by RTP.

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  Fig. 2. Cryo-EM structure of the apo nsp12-nsp-7-nsp8 RdRp complex. (A and B) Two views of the cryo-EM map (A) and structure (B) of the apo nsp12-nsp7-nsp8 complex. The color scheme is according to Fig. 1A and is used throughout the figures. (C) The conserved zinc binding motifs are highlighted in the apo structure rendered in ribbon. The coordinate details of the zinc-binding residues are shown in stick representation, with the EM map in gray surface representation.

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  Fig. 3. Cryo-EM structure of the remdesivir- and RNA-bound RdRp complex. (A and B) Two views of the cryo-EM map (A) and structure (B) of nsp12-nsp7-nsp8 in complex with template-primer RNA and remdesivir. (C) Surface view of the RdRp active site with the electrostatic potential from red (negative) to blue (positive). For clarity, residues 410 to 442 and 834 to 919 of nsp12 and nsp8 are excluded from the figure. The covalently bound remdesivir in the monophosphate form and the product, pyrophosphate, are shown. The active site is emphasized with a yellow dashed circle. The template groove, the entrance for nucleotide triphosphate (NTP), and the elongation direction are annotated with different-colored arrows. (D) Close-up view of the RdRp active site, showing the covalently bound RMP, pyrophosphate, and magnesium ions. Key residues and bases that interact with remdesivir are shown. (E and F) Superposition of the conserved RdRp motifs (A to G) of the RNA-bound complex with the apo structure (colored in gray), with a close-up view at the active site (E) and at the exit of the template and primer strand (F).

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  Fig. 4. RNA recognition by the RdRp complex. (A to D) Protein-RNA interactions in the RNA- and remdesivir-bound RdRp complex. (E) Diagram of detailed RNA interactions with RdRp. Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.