EMD-40708

Composite map
Single-particle
3.01 Å
EMD-40708 Deposition: 04/05/2023
Map released: 22/11/2023
Last modified: 25/12/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-40708

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

EMD-40708

Composite map
Single-particle
3.01 Å
EMD-40708 Deposition: 04/05/2023
Map released: 22/11/2023
Last modified: 25/12/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Severe acute respiratory syndrome coronavirus 2, Severe acute respiratory syndrome coronavirus
Sample: SARS-CoV-2 replication-transcription complex bound to RNA-nsp9 and GDP-betaS, as a pre-catalytic deRNAylation/mRNA capping intermediate
Fitted models: 8sqk (Avg. Q-score: 0.533)

Deposition Authors: Small GI, Darst SA, Campbell EA
Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain.
PUBMED: 37890482
DOI: doi:10.1016/j.molcel.2023.10.001
ISSN: 1097-2765
ASTM: MOCEFL
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.