8SQK

SARS-CoV-2 replication-transcription complex bound to RNA-nsp9 and GDP-betaS, as a pre-catalytic deRNAylation/mRNA capping intermediate

Summary for 8SQK

• Entry DOI: 10.2210/pdb8sqk/pdb
• Related: 8SQ9 8SQJ
• EMDB information: 40699 40707 40708
• Descriptor: RNA-directed RNA polymerase nsp12, MAGNESIUM ION, Non-structural protein 8, ... (11 entities in total)
• Functional Keywords: rtc, nsp12, nsp9, niran, sars-cov-2, dernaylation, mrna capping, umpcpp, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2; More
• Total number of polymer chains: 8
• Total formula weight: 200705.81

Authors

Small, G.I.,Darst, S.A.,Campbell, E.A. (deposition date: 2023-05-04, release date: 2023-11-22, Last modification date: 2025-05-21)

Primary citation

Small, G.I.,Fedorova, O.,Olinares, P.D.B.,Chandanani, J.,Banerjee, A.,Choi, Y.J.,Molina, H.,Chait, B.T.,Darst, S.A.,Campbell, E.A.
Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain.
Mol.Cell, 83:3921-3930.e7, 2023

PubMed Abstract: The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5' cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here, we determine high-resolution cryoelectron microscopy (cryo-EM) structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.

PubMed: 37890482
DOI: 10.1016/j.molcel.2023.10.001

Experimental method

ELECTRON MICROSCOPY (3.01 Å)