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

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.

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/nsp8(2)/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-Mg(2+) bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapeutic development.