2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography

Proc Natl Acad Sci U S A. 2021 May 25;118(21):e2100170118. doi: 10.1073/pnas.2100170118.


The genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus has a capping modification at the 5'-untranslated region (UTR) to prevent its degradation by host nucleases. These modifications are performed by the Nsp10/14 and Nsp10/16 heterodimers using S-adenosylmethionine as the methyl donor. Nsp10/16 heterodimer is responsible for the methylation at the ribose 2'-O position of the first nucleotide. To investigate the conformational changes of the complex during 2'-O methyltransferase activity, we used a fixed-target serial synchrotron crystallography method at room temperature. We determined crystal structures of Nsp10/16 with substrates and products that revealed the states before and after methylation, occurring within the crystals during the experiments. Here we report the crystal structure of Nsp10/16 in complex with Cap-1 analog (m7GpppAm2'-O). Inhibition of Nsp16 activity may reduce viral proliferation, making this protein an attractive drug target.

Keywords: CAP-1; Nsp10/16; SARS-CoV-2; mRNA; serial crystallography.

Publication types

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

MeSH terms

  • Crystallography
  • Methylation
  • Methyltransferases / chemistry
  • Methyltransferases / metabolism
  • Multiprotein Complexes / chemistry
  • Multiprotein Complexes / metabolism
  • RNA Cap Analogs / chemistry
  • RNA Cap Analogs / metabolism
  • RNA Caps / chemistry
  • RNA Caps / metabolism*
  • RNA, Messenger / chemistry
  • RNA, Messenger / metabolism*
  • RNA, Viral / chemistry
  • RNA, Viral / metabolism*
  • S-Adenosylhomocysteine / chemistry
  • S-Adenosylhomocysteine / metabolism
  • S-Adenosylmethionine / chemistry
  • S-Adenosylmethionine / metabolism
  • SARS-CoV-2 / chemistry*
  • SARS-CoV-2 / genetics
  • SARS-CoV-2 / metabolism
  • Synchrotrons
  • Viral Nonstructural Proteins / chemistry
  • Viral Nonstructural Proteins / metabolism
  • Viral Regulatory and Accessory Proteins / chemistry
  • Viral Regulatory and Accessory Proteins / metabolism


  • Multiprotein Complexes
  • NSP10 protein, SARS-CoV-2
  • NSP16 protein, SARS-CoV-2
  • RNA Cap Analogs
  • RNA Caps
  • RNA, Messenger
  • RNA, Viral
  • Viral Nonstructural Proteins
  • Viral Regulatory and Accessory Proteins
  • S-Adenosylmethionine
  • S-Adenosylhomocysteine
  • Methyltransferases
  • cap I RNA (nucleoside-2'-)methyltransferase