SNAP output for PDB entry 7uo7 [SNAP web server]

PDB-id

7uo7; SNAP-derived features in text and JSON formats; DNAproDB

Class

replication

Method

cryo-EM (3.09 Å)

Summary

Sars-cov-2 replication-transcription complex bound to atp, in a pre-catalytic state

Reference

Malone BF, Perry JK, Olinares PDB, Lee HW, Chen J, Appleby TC, Feng JY, Bilello JP, Ng H, Sotiris J, Ebrahim M, Chua EYD, Mendez JH, Eng ET, Landick R, Gotte M, Chait BT, Campbell EA, Darst SA (2023): "Structural basis for substrate selection by the SARS-CoV-2 replicase." Nature, 614, 781-787. doi: 10.1038/s41586-022-05664-3.

Abstract

The SARS-CoV-2 RNA-dependent RNA polymerase coordinates viral RNA synthesis as part of an assembly known as the replication-transcription complex (RTC)₁. Accordingly, the RTC is a target for clinically approved antiviral nucleoside analogues, including remdesivir₂. Faithful synthesis of viral RNAs by the RTC requires recognition of the correct nucleotide triphosphate (NTP) for incorporation into the nascent RNA. To be effective inhibitors, antiviral nucleoside analogues must compete with the natural NTPs for incorporation. How the SARS-CoV-2 RTC discriminates between the natural NTPs, and how antiviral nucleoside analogues compete, has not been discerned in detail. Here, we use cryogenic-electron microscopy to visualize the RTC bound to each of the natural NTPs in states poised for incorporation. Furthermore, we investigate the RTC with the active metabolite of remdesivir, remdesivir triphosphate (RDV-TP), highlighting the structural basis for the selective incorporation of RDV-TP over its natural counterpart adenosine triphosphate_3,4. Our results explain the suite of interactions required for NTP recognition, informing the rational design of antivirals. Our analysis also yields insights into nucleotide recognition by the nsp12 NiRAN (nidovirus RdRp-associated nucleotidyltransferase), an enigmatic catalytic domain essential for viral propagation₅. The NiRAN selectively binds guanosine triphosphate, strengthening proposals for the role of this domain in the formation of the 5' RNA cap₆.