9IKZ

SARS-CoV-2 E-RTC bound to pRNA-nsp9 and GDP-BeF3-

Summary for 9IKZ

• Entry DOI: 10.2210/pdb9ikz/pdb
• EMDB information: 60663
• Descriptor: RNA-directed RNA polymerase nsp12, BERYLLIUM TRIFLUORIDE ION, MAGNESIUM ION, ... (11 entities in total)
• Functional Keywords: sars-cov-2, rtc, nsp12, nsp13, nsp9, gdp-bef3-, viral protein/rna, viral protein-rna complex
• Biological source: Severe acute respiratory syndrome coronavirus 2; More
• Total number of polymer chains: 9
• Total formula weight: 319060.41

Authors

Yan, L.M.,Huang, Y.C.,Liu, Y.X.,Rao, Z.H.,Lou, Z.Y. (deposition date: 2024-06-29, release date: 2025-06-18, Last modification date: 2025-12-31)

Primary citation

Huang, Y.,Tan, L.,Liu, Y.,Zhao, H.,Wang, J.,Ge, J.,Ye, S.,Liu, Z.,Lan, W.,Huang, B.,Zhang, H.,Gao, Y.,Yan, L.,Rao, Z.,Lou, Z.
Response to: The mechanism for GTP-mediated RNA capping by the SARS-CoV-2 NiRAN domain remains unresolved.
Cell, 188:4462-4469.e9, 2025

PubMed Abstract: 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.

PubMed: 40570837
DOI: 10.1016/j.cell.2025.05.045

Experimental method

ELECTRON MICROSCOPY (3.14 Å)