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TitleStructural Basis for RNA Replication by the SARS-CoV-2 Polymerase.
Journal, issue, pagesCell, Vol. 182, Issue 2, Page 417-428.e13, Year 2020
Publish dateJul 23, 2020
AuthorsQuan Wang / Jiqin Wu / Haofeng Wang / Yan Gao / Qiaojie Liu / An Mu / Wenxin Ji / Liming Yan / Yan Zhu / Chen Zhu / Xiang Fang / Xiaobao Yang / Yucen Huang / Hailong Gao / Fengjiang Liu / Ji Ge / Qianqian Sun / Xiuna Yang / Wenqing Xu / Zhijie Liu / Haitao Yang / Zhiyong Lou / Biao Jiang / Luke W Guddat / Peng Gong / Zihe Rao /
PubMed AbstractNucleotide analog inhibitors, including broad-spectrum remdesivir and favipiravir, have shown promise in in vitro assays and some clinical studies for COVID-19 treatment, this despite an incomplete ...Nucleotide analog inhibitors, including broad-spectrum remdesivir and favipiravir, have shown promise in in vitro assays and some clinical studies for COVID-19 treatment, this despite an incomplete mechanistic understanding of the viral RNA-dependent RNA polymerase nsp12 drug interactions. Here, we examine the molecular basis of SARS-CoV-2 RNA replication by determining the cryo-EM structures of the stalled pre- and post- translocated polymerase complexes. Compared with the apo complex, the structures show notable structural rearrangements happening to nsp12 and its co-factors nsp7 and nsp8 to accommodate the nucleic acid, whereas there are highly conserved residues in nsp12, positioning the template and primer for an in-line attack on the incoming nucleotide. Furthermore, we investigate the inhibition mechanism of the triphosphate metabolite of remdesivir through structural and kinetic analyses. A transition model from the nsp7-nsp8 hexadecameric primase complex to the nsp12-nsp7-nsp8 polymerase complex is also proposed to provide clues for the understanding of the coronavirus transcription and replication machinery.
External linksCell / PubMed:32526208 / PubMed Central
MethodsEM (single particle)
Resolution2.93 - 3.26 Å
Structure data

30252

7bzf

EMDB-30252, PDB-7bzf:
COVID-19 RNA-dependent RNA polymerase post-translocated catalytic complex
Method: EM (single particle) / Resolution: 3.26 Å

30275

7c2k

EMDB-30275, PDB-7c2k:
COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex
Method: EM (single particle) / Resolution: 2.93 Å

EMDB-30283:
COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex in conformation I
Method: EM (single particle) / Resolution: 3.03 Å

EMDB-30284:
COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex in conformation II
Method: EM (single particle) / Resolution: 3.12 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • severe acute respiratory syndrome coronavirus 2
  • foot-and-mouth disease virus
KeywordsVIRAL PROTEIN/RNA / COVID-19 / 2019-nCoV / SARS-CoV-2 / Virus / RdRp / nsp12 / nsp7 / nsp8 / RTC / cryo-EM / Viral protein / RNA polymerase / drug target / antiviral / replication transcription complex / VIRAL PROTEIN-RNA complex / pre-translocated catalytic complex

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