Crystal structure of SARS-CoV-2 nsp10 bound to nsp14-ExoN domain reveals an exoribonuclease with both structural and functional integrity

Nucleic Acids Res. 2021 May 21;49(9):5382-5392. doi: 10.1093/nar/gkab320.


The emergence of SARS-CoV-2 infection has posed unprecedented threat to global public health. The virus-encoded non-structural protein 14 (nsp14) is a bi-functional enzyme consisting of an exoribonuclease (ExoN) domain and a methyltransferase (MTase) domain and plays a pivotal role in viral replication. Here, we report the structure of SARS-CoV-2 nsp14-ExoN domain bound to its co-factor nsp10 and show that, compared to the SARS-CoV nsp10/nsp14-full-length complex, SARS-CoV-2 nsp14-ExoN retains an integral exoribonuclease fold and preserves an active configuration in the catalytic center. Analysis of the nsp10/nsp14-ExoN interface reveals a footprint in nsp10 extensively overlapping with that observed in the nsp10/nsp16 structure. A marked difference in the co-factor when engaging nsp14 and nsp16 lies in helix-α1', which is further experimentally ascertained to be involved in nsp14-binding but not in nsp16-engagement. Finally, we also show that nsp10/nsp14-ExoN is enzymatically active despite the absence of nsp14-MTase domain. These data demonstrate that SARS-CoV-2 nsp10/nsp14-ExoN functions as an exoribonuclease with both structural and functional integrity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Biocatalysis*
  • Crystallography, X-Ray
  • Exoribonucleases / chemistry*
  • Exoribonucleases / genetics
  • Exoribonucleases / metabolism*
  • Guanine
  • Methyltransferases / chemistry
  • Methyltransferases / deficiency
  • Methyltransferases / genetics
  • Methyltransferases / metabolism
  • Models, Molecular
  • Protein Domains / genetics
  • SARS-CoV-2 / chemistry*
  • SARS-CoV-2 / enzymology*
  • SARS-CoV-2 / genetics
  • Viral Nonstructural Proteins / chemistry*
  • Viral Nonstructural Proteins / genetics
  • Viral Nonstructural Proteins / metabolism*
  • Viral Regulatory and Accessory Proteins / chemistry*
  • Viral Regulatory and Accessory Proteins / genetics
  • Viral Regulatory and Accessory Proteins / metabolism*


  • NSP10 protein, SARS-CoV-2
  • NSP16 protein, SARS-CoV-2
  • Viral Nonstructural Proteins
  • Viral Regulatory and Accessory Proteins
  • Guanine
  • Methyltransferases
  • Exoribonucleases
  • NSP14 protein, SARS-CoV-2