Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex

Cell. 2020 Sep 17;182(6):1560-1573.e13. doi: 10.1016/j.cell.2020.07.033. Epub 2020 Jul 28.


SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated and 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 cryoelectron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template product in complex with two molecules of the nsp13 helicase. The Nidovirales 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 therapy development.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Diphosphate / chemistry
  • Adenosine Diphosphate / metabolism
  • Betacoronavirus / genetics
  • Betacoronavirus / metabolism
  • Betacoronavirus / ultrastructure
  • Binding Sites
  • Coronavirus RNA-Dependent RNA Polymerase
  • Cryoelectron Microscopy
  • Holoenzymes / chemistry
  • Holoenzymes / metabolism
  • Magnesium / metabolism
  • Methyltransferases / chemistry*
  • Methyltransferases / metabolism
  • Protein Binding
  • RNA Helicases / chemistry*
  • RNA Helicases / metabolism
  • RNA, Viral / chemistry
  • RNA-Dependent RNA Polymerase / chemistry*
  • RNA-Dependent RNA Polymerase / metabolism
  • SARS-CoV-2
  • Viral Nonstructural Proteins / chemistry*
  • Viral Nonstructural Proteins / metabolism
  • Virus Replication*


  • Holoenzymes
  • NS8 protein, SARS-CoV-2
  • RNA, Viral
  • Viral Nonstructural Proteins
  • Adenosine Diphosphate
  • Methyltransferases
  • Nsp13 protein, SARS-CoV
  • Coronavirus RNA-Dependent RNA Polymerase
  • NSP12 protein, SARS-CoV-2
  • NSP7 protein, SARS-CoV-2
  • RNA-Dependent RNA Polymerase
  • RNA Helicases
  • Magnesium