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Structure paper

TitleStructural basis for backtracking by the SARS-CoV-2 replication-transcription complex.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 118, Issue 19, Year 2021
Publish dateMay 11, 2021
AuthorsBrandon Malone / James Chen / Qi Wang / Eliza Llewellyn / Young Joo Choi / Paul Dominic B Olinares / Xinyun Cao / Carolina Hernandez / Edward T Eng / Brian T Chait / David E Shaw / Robert Landick / Seth A Darst / Elizabeth A Campbell /
PubMed AbstractBacktracking, the reverse motion of the transcriptase enzyme on the nucleic acid template, is a universal regulatory feature of transcription in cellular organisms but its role in viruses is not ...Backtracking, the reverse motion of the transcriptase enzyme on the nucleic acid template, is a universal regulatory feature of transcription in cellular organisms but its role in viruses is not established. Here we present evidence that backtracking extends into the viral realm, where backtracking by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) may aid viral transcription and replication. Structures of SARS-CoV-2 RdRp bound to the essential nsp13 helicase and RNA suggested the helicase facilitates backtracking. We use cryo-electron microscopy, RNA-protein cross-linking, and unbiased molecular dynamics simulations to characterize SARS-CoV-2 RdRp backtracking. The results establish that the single-stranded 3' segment of the product RNA generated by backtracking extrudes through the RdRp nucleoside triphosphate (NTP) entry tunnel, that a mismatched nucleotide at the product RNA 3' end frays and enters the NTP entry tunnel to initiate backtracking, and that nsp13 stimulates RdRp backtracking. Backtracking may aid proofreading, a crucial process for SARS-CoV-2 resistance against antivirals.
External linksProc Natl Acad Sci U S A / PubMed:33883267 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 3.6 Å
Structure data

EMDB-23007, PDB-7krn:
Structure of SARS-CoV-2 backtracked complex bound to nsp13 helicase - nsp13(1)-BTC
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-23008, PDB-7kro:
Structure of SARS-CoV-2 backtracked complex complex bound to nsp13 helicase - nsp13(2)-BTC
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-23009, PDB-7krp:
Structure of SARS-CoV-2 backtracked complex complex bound to nsp13 helicase - BTC (local refinement)
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-ZN:
ZINC ION / Zinc

ChemComp-MG:
MAGNESIUM ION / Magnesium

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-1N7:
CHAPSO / detergent*YM / CHAPS detergent

ChemComp-AF3:
ALUMINUM FLUORIDE / Aluminium fluoride

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsAdenosine Monophosphate / Antiviral Agents / COVID-19 / Coronavirus RNA-Dependent RNA Polymerase / Cryoelectron Microscopy / DNA Helicases / Genome, Viral / Humans / Molecular Dynamics Simulation / RNA Helicases / RNA, Viral / RNA-Dependent RNA Polymerase / SARS-CoV-2 / Viral Nonstructural Proteins / Virus Replication / TRANSFERASE/HYDROLASE/RNA / viral replication-transcription complex / transcription / viral proteins / TRANSFERASE-HYDROLASE-RNA complex / TRANSFERASE/RNA / TRANSFERASE-RNA complex

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