SNAP output for PDB entry 8gwk [SNAP web server]

PDB-id

8gwk; SNAP-derived features in text and JSON formats; DNAproDB

Class

viral protein-inhibitor

Method

cryo-EM (2.72 Å)

Summary

Sars-cov-2 RNA e-rtc complex with rmp-nsp9 and gmppnp

Reference

Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z (2022): "A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors." Cell, 185, 4347-4360.e17. doi: 10.1016/j.cell.2022.09.037.

Abstract

Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The NiRAN domain in polymerase catalyzes the covalent link of RNA 5' end to the first residue of nsp9 (termed as RNAylation), thus being an intermediate to form cap core (GpppA) with GTP catalyzed again by NiRAN. We also reveal that triphosphorylated nucleotide analog inhibitors can be bonded to nsp9 and fit into a previously unknown "Nuc-pocket" in NiRAN, thus inhibiting nsp9 RNAylation and formation of GpppA. S-loop (residues 50-KTN-52) in NiRAN presents a remarkable conformational shift observed in RTC bound with sofosbuvir monophosphate, reasoning an "induce-and-lock" mechanism to design inhibitors. These findings not only improve the understanding of SARS-CoV-2 RNA capping and the mode of action of NAIs but also provide a strategy to design antiviral drugs.