SNAP output for PDB entry 7aap [SNAP web server]

PDB-id

7aap; SNAP-derived features in text and JSON formats; DNAproDB

Class

viral protein

Method

cryo-EM (2.5 Å)

Summary

Nsp7-nsp8-nsp12 sars-cov2 RNA-dependent RNA polymerase in complex with template:primer dsrna and favipiravir-rtp

Reference

Naydenova K, Muir KW, Wu LF, Zhang Z, Coscia F, Peet MJ, Castro-Hartmann P, Qian P, Sader K, Dent K, Kimanius D, Sutherland JD, Lowe J, Barford D, Russo CJ (2021): "Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2021946118.

Abstract

The RNA polymerase inhibitor favipiravir is currently in clinical trials as a treatment for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, nonproductive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp, which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.