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TitleStructural basis for the concurrence of template recycling and RNA capping in SARS-CoV-2.
Journal, issue, pagesCell, Vol. 188, Issue 25, Page 7194-7205.e10, Year 2025
Publish dateDec 11, 2025
AuthorsLiming Yan / Yucen Huang / Yixiao Liu / Ji Ge / Shan Gao / Liping Tan / Lu Liu / Zhenyu Liu / Sihan Ye / Junbo Wang / Jiangran Xiong / Yu Zhou / Hesheng Zhao / Xiaoyue Zhao / Luke W Guddat / Yan Gao / Lan Zhu / Zihe Rao / Zhiyong Lou /
PubMed AbstractIn the SARS-CoV-2 replication-transcription complex (RTC), the nascent template-product duplex is unwound into a template strand for recycling and a product strand that needs to be capped. Here, we ...In the SARS-CoV-2 replication-transcription complex (RTC), the nascent template-product duplex is unwound into a template strand for recycling and a product strand that needs to be capped. Here, we determined structures of the SARS-CoV-2 RTC in the pre- and post-capping initiation (CI) states. In the pre-CI state, the RTC has a dimer-of-dimeric architecture (ddRTC). The upstream RNA duplex in one RTC is reciprocally unwound by a helicase in a head-to-head-positioned RTC in the 3'-5' direction. The helicases bind either ADP or ADP⋅P in their ATP-binding pockets, suggesting a mechanism for ATP-hydrolysis-driven unwinding. In the post-CI state, the binding of nsp9 to the nsp12 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) disrupts the ddRTC. The N terminus of nsp9 and the triphosphorylated 5' end of the product strand co-localize in NiRAN's catalytic site, exhibiting the state prior to nsp9 RNAylation for capping. These results provide an insight into the concurrence of template recycling and RNA capping in the SARS-CoV-2 RTC.
External linksCell / PubMed:41130208
MethodsEM (single particle)
Resolution3.01 - 4.01 Å
Structure data

38243

8xch

EMDB-38243, PDB-8xch:
SARS-CoV-2 Replication-Transcription Complex has a dimer-of-dimeric architecture (ddRTC) in pre-capping initiation.
Method: EM (single particle) / Resolution: 3.4 Å

60692

9imk

EMDB-60692, PDB-9imk:
SARS-CoV-2 Replication-Transcription Complex has a dimer architecture (dRTC) in post-capping state
Method: EM (single particle) / Resolution: 4.01 Å

60693

9imm

EMDB-60693, PDB-9imm:
SARS-CoV-2 Replication-Transcription Complex has a dimer architecture (local dRTC) in post-capping state
Method: EM (single particle) / Resolution: 3.22 Å

EMDB-62623: Local map(dC-RTC) of pre-CI RTC
Method: EM (single particle) / Resolution: 3.01 Å

EMDB-62625: nsp13-1 bound with RNA(local map of pre CI RTC)
Method: EM (single particle) / Resolution: 3.51 Å

EMDB-62638: nsp13-2 bound with RNA(local map of pre-CI RTC)
Method: EM (single particle) / Resolution: 3.43 Å

EMDB-62639: nsp13-1 apo(local map of Pre-CI RTC)
Method: EM (single particle) / Resolution: 3.21 Å

Chemicals

ChemComp-ZN:
Unknown entry

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

ChemComp-MG:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION

ChemComp-HOH:
WATER

Source
  • severe acute respiratory syndrome coronavirus 2
  • synthetic construct (others)
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Replication-Transcription Complex / helicase / RNA unwinding / cryo-EM / VIRAL PROTEIN/RNA / unwinding / RNA capping / VIRAL PROTEIN-RNA complex / SARS-2 / nsp9 / pppRNA

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