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TitleResponse to: The mechanism for GTP-mediated RNA capping by the SARS-CoV-2 NiRAN domain remains unresolved.
Journal, issue, pagesCell, Vol. 188, Issue 16, Page 4462-44469.e9, Year 2025
Publish dateAug 7, 2025
AuthorsYucen Huang / Liping Tan / Yixiao Liu / Hesheng Zhao / Junbo Wang / Ji Ge / Sihan Ye / Zhenyu Liu / Weiqi Lan / Bo Huang / Hongbo Zhang / Yan Gao / Liming Yan / Zihe Rao / Zhiyong Lou /
PubMed AbstractThe SARS-CoV-2 polymerase NiRAN domain initiates RNA capping. Previous results showed that both GTP and GDP can be utilized by NiRAN to yield GpppA together with RNAylated nsp9 (RNA-nsp9); however, ...The SARS-CoV-2 polymerase NiRAN domain initiates RNA capping. Previous results showed that both GTP and GDP can be utilized by NiRAN to yield GpppA together with RNAylated nsp9 (RNA-nsp9); however, the G-pocket substrate selection and the working mechanism of NiRAN remain unclear. Small et al. questioned the binding of the non-hydrolyzable GTP analog GMPPNP in the G-pocket of the RTC:RNA-nsp9:GMPPNP structure (PDB: 8GWE) and proposed that the GTP-mediated RNA-capping mechanism remains unresolved. Here, we show the optimized density derived from the original data to support the modeling of GMPPNP, and we reveal why the alternative data processing method failed to obtain density results. We provide additional biochemical and structural evidence by using GTP, GDP, GMPPNP, and GDP⋅BeF as probes to clarify the GTP-mediated RNA-capping mechanism and reconcile the two currently known models by using GTP and GDP as substrates. This Matters Arising Response addresses the Small et al. (2025) Matters Arising paper, published concurrently in Cell.
External linksCell / PubMed:40570837
MethodsEM (single particle)
Resolution3.14 Å
Structure data

60663

9ikz

EMDB-60663, PDB-9ikz:
SARS-CoV-2 E-RTC bound to pRNA-nsp9 and GDP-BeF3-
Method: EM (single particle) / Resolution: 3.14 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-MG:
Unknown entry

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN/RNA / SARS-CoV-2 / RTC / nsp12 / nsp13 / nsp9 / GDP-BeF3- / VIRAL PROTEIN-RNA complex

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