PDBsum entry 7b3c

Viral protein

PDB id: 7b3c

Contents

Protein chains

814 a.a.

115 a.a.

62 a.a.

DNA/RNA

Metals

_ZN ×2

PDB id:

7b3c

Name:

Viral protein

Title:

Structure of elongating sars-cov-2 RNA-dependent RNA polymerase with remdesivir at position -4 (structure 2)

Structure:

RNA-directed RNA polymerase nsp12. Chain: a. Synonym: pol,rdrp,non-structural protein 12,nsp12. Engineered: yes. Non-structural protein 8. Chain: b. Synonym: nsp8. Engineered: yes. Non-structural protein 7.

Source:

Severe acute respiratory syndrome coronavirus 2. Organism_taxid: 2697049. Gene: rep, 1a-1b. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: ril.

Authors:

G.Kokic,H.S.Hillen,D.Tegunov,C.Dienemann,F.Seitz,J.Schmitzova, L.Farnung,A.Siewert,C.Hoebartner,P.Cramer

Key ref:

G.Kokic et al. (2021). Mechanism of SARS-CoV-2 polymerase stalling by remdesivir. Nat Commun, 12, 279. PubMed id: 33436624 DOI: 10.1038/s41467-020-20542-0

Date:

30-Nov-20 Release date: 23-Dec-20

Protein chain

P0DTD1  (R1AB_SARS2) -

Protein chain

P0DTD1  (R1AB_SARS2) -

Protein chain

P0DTD1  (R1AB_SARS2) -

DNA/RNA chains

C-C-U-A-C-G-C-F86-G-U-G 11 bases

G-C-A-C-U-G-C-G-U-A-G-G 12 bases

Enzyme reactions

• Enzyme class: Chain A: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1038/s41467-020-20542-0

Nat Commun 12:279 (2021)

PubMed id: 33436624

Mechanism of SARS-CoV-2 polymerase stalling by remdesivir.

G.Kokic, H.S.Hillen, D.Tegunov, C.Dienemann, F.Seitz, J.Schmitzova, L.Farnung, A.Siewert, C.Höbartner, P.Cramer.

ABSTRACT

Remdesivir is the only FDA-approved drug for the treatment of COVID-19 patients. The active form of remdesivir acts as a nucleoside analog and inhibits the RNA-dependent RNA polymerase (RdRp) of coronaviruses including SARS-CoV-2. Remdesivir is incorporated by the RdRp into the growing RNA product and allows for addition of three more nucleotides before RNA synthesis stalls. Here we use synthetic RNA chemistry, biochemistry and cryo-electron microscopy to establish the molecular mechanism of remdesivir-induced RdRp stalling. We show that addition of the fourth nucleotide following remdesivir incorporation into the RNA product is impaired by a barrier to further RNA translocation. This translocation barrier causes retention of the RNA 3'-nucleotide in the substrate-binding site of the RdRp and interferes with entry of the next nucleoside triphosphate, thereby stalling RdRp. In the structure of the remdesivir-stalled state, the 3'-nucleotide of the RNA product is matched and located with the template base in the active center, and this may impair proofreading by the viral 3'-exonuclease. These mechanistic insights should facilitate the quest for improved antivirals that target coronavirus replication.