Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex

• Published in: bioRxiv
• Main Authors: Chen, James, Malone, Brandon, Llewellyn, Eliza, Grasso, Michael, Shelton, Patrick M M, Olinares, Paul Dominic B, Maruthi, Kashyap, Eng, Ed, Vatandaslar, Hasan, Chait, Brian T, Kapoor, Tarun, Darst, Seth A, Campbell, Elizabeth A
• Format: Journal Article Paper
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 13.07.2020
• Subjects: Adenosine triphosphatase; Antiviral agents; COVID-19; DNA helicase; DNA-directed RNA polymerase; Genomes; Magnesium; Pandemics; Replication; RNA polymerase; RNA-directed RNA polymerase; Severe acute respiratory syndrome coronavirus 2; Transcription
• DOI: 10.1101/2020.07.08.194084

SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated-transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase. Both the holo-RdRp and nsp13 are essential for viral replication and are targets for treating the disease COVID-19. Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The Nidovirus-order-specific N-terminal domains of each nsp13 interact with the N-terminal extension of each copy of nsp8. One nsp13 also contacts the nsp12-thumb. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. We also observe ADP-Mg2+ bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapeutic development.