Modomics - A Database of RNA Modifications

ID Card:

Full name: 2'-O-methyltransferase nsp16
Structures: | 6W4H | 6W75 | 6W61 |
Complex: nsp10
Enzyme type: methyltransferase

PDB Structures:


Structure Description:


Abstract of the PDB Structure's related Publication:

There are currently no antiviral therapies specific for SARS-CoV-2, the virus responsible for the global pandemic disease COVID-19. To facilitate structure-based drug design, we conducted an x-ray crystallographic study of the SARS-CoV-2 nsp16-nsp10 2'- O -methyltransferase complex, which methylates Cap-0 viral mRNAs to improve viral protein translation and to avoid host immune detection. We determined the structures for nsp16-nsp10 heterodimers bound to the methyl donor S -adenosylmethionine (SAM), the reaction product S -adenosylhomocysteine (SAH), or the SAH analog sinefungin (SFG). We also solved structures for nsp16-nsp10 in complex with the methylated Cap-0 analog m 7 GpppA and either SAM or SAH. Comparative analyses between these structures and published structures for nsp16 from other betacoronaviruses revealed flexible loops in open and closed conformations at the m 7 GpppA-binding pocket. Bound sulfates in several of the structures suggested the location of the ribonucleic acid backbone phosphates in the ribonucleotide-binding groove. Additional nucleotide-binding sites were found on the face of the protein opposite the active site. These various sites and the conserved dimer interface could be exploited for the development of antiviral inhibitors.

Download RCSB-PDB Structures:

Pdb Files   6W4H.pdb   6W61.pdb   6W75.pdb  
Pdbx/mmCIF Files   6W4H.cif   6W61.cif   6W75.cif  

Protein sequence:



2'-O-methyltransferase complex of the SARS-CoV-2 coronavirus which mediates mRNA cap 2'-O-ribose methylation at first transcribed nucleotide of viral mRNAs. nsp16 uses S-adenosyl-L-methionine as the methyl donor.


Title Authors Journal Details PubMed Id DOI
Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. Petra Krafcikova,Jan Silhan,Radim Nencka,Evzen Boura Nat Commun [details] 32709887 -
High-resolution structures of the SARS-CoV-2 2'--methyltransferase reveal strategies for structure-based inhibitor design. Monica Rosas-Lemus,George Minasov,Ludmilla Shuvalova,Nicole L Inniss,Olga Kiryukhina,Joseph Brunzelle,Karla J F Satchell Sci Signal [details] 32994211 -