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TitleEnsemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex.
Journal, issue, pagesNat Struct Mol Biol, Vol. 29, Issue 3, Page 250-260, Year 2022
Publish dateMar 8, 2022
AuthorsJames Chen / Qi Wang / Brandon Malone / Eliza Llewellyn / Yakov Pechersky / Kashyap Maruthi / Ed T Eng / Jason K Perry / Elizabeth A Campbell / David E Shaw / Seth A Darst /
PubMed AbstractThe SARS-CoV-2 nonstructural proteins coordinate genome replication and gene expression. Structural analyses revealed the basis for coupling of the essential nsp13 helicase with the RNA-dependent RNA ...The SARS-CoV-2 nonstructural proteins coordinate genome replication and gene expression. Structural analyses revealed the basis for coupling of the essential nsp13 helicase with the RNA-dependent RNA polymerase (RdRp) where the holo-RdRp and RNA substrate (the replication-transcription complex or RTC) associated with two copies of nsp13 (nsp13-RTC). One copy of nsp13 interacts with the template-RNA in an opposing polarity to the RdRp and is envisaged to drive the RdRp backward on the RNA template (backtracking), prompting questions as to how the RdRp can efficiently synthesize RNA in the presence of nsp13. Here we use cryogenic-electron microscopy and molecular dynamics simulations to analyze the nsp13-RTC, revealing four distinct conformational states of the helicases. The results indicate a mechanism for the nsp13-RTC to turn backtracking on and off, using an allosteric mechanism to switch between RNA synthesis or backtracking in response to stimuli at the RdRp active site.
External linksNat Struct Mol Biol / PubMed:35260847 / PubMed Central
MethodsEM (single particle)
Resolution2.91 - 3.6 Å
Structure data

EMDB-24426, PDB-7rdx:
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - open class
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-24427, PDB-7rdy:
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - engaged class
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-24428, PDB-7rdz:
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - apo class
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-24429, PDB-7re0:
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - swiveled class
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-24430, PDB-7re1:
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC (composite)
Method: EM (single particle) / Resolution: 2.91 Å

EMDB-24431, PDB-7re2:
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(1)-RTC
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-24432, PDB-7re3:
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC dimer
Method: EM (single particle) / Resolution: 3.33 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

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

ChemComp-1N7:
CHAPSO / detergent*YM

ChemComp-AF3:
ALUMINUM FLUORIDE

ChemComp-HOH:
WATER

Source
  • severe acute respiratory syndrome coronavirus 2
  • synthetic construct (others)
KeywordsREPLICATION/TRANSCRIPTION / RNA-dependent RNA polymerase / viral replication-transcription complex / transcription / viral proteins / REPLICATION-TRANSCRIPTION complex

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