7THM

SARS-CoV-2 nsp12/7/8 complex with a native N-terminus nsp9

Summary for 7THM

• Entry DOI: 10.2210/pdb7thm/pdb
• EMDB information: 25898
• Descriptor: RNA-directed RNA polymerase, Non-structural protein 8, Non-structural protein 7, ... (7 entities in total)
• Functional Keywords: polymerase, niran, capping, nsp9, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2); More
• Total number of polymer chains: 5
• Total formula weight: 172588.76

Authors

Osinski, A.,Tagliabracci, V.S.,Chen, Z.,Li, Y. (deposition date: 2022-01-11, release date: 2022-03-16, Last modification date: 2025-05-28)

Primary citation

Park, G.J.,Osinski, A.,Hernandez, G.,Eitson, J.L.,Majumdar, A.,Tonelli, M.,Henzler-Wildman, K.,Pawlowski, K.,Chen, Z.,Li, Y.,Schoggins, J.W.,Tagliabracci, V.S.
The mechanism of RNA capping by SARS-CoV-2.
Nature, 609:793-800, 2022

PubMed Abstract: The RNA genome of SARS-CoV-2 contains a 5' cap that facilitates the translation of viral proteins, protection from exonucleases and evasion of the host immune response. How this cap is made in SARS-CoV-2 is not completely understood. Here we reconstitute the N7- and 2'-O-methylated SARS-CoV-2 RNA cap (GpppA) using virally encoded non-structural proteins (nsps). We show that the kinase-like nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain of nsp12 transfers the RNA to the amino terminus of nsp9, forming a covalent RNA-protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers the RNA to GDP, forming the core cap structure GpppA-RNA. The nsp14 and nsp16 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication-transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system that the N terminus of nsp9 and the kinase-like active-site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19.

PubMed: 35944563
DOI: 10.1038/s41586-022-05185-z

Experimental method

ELECTRON MICROSCOPY (3.18 Å)