8SQK

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

8SQK の概要

• エントリーDOI: 10.2210/pdb8sqk/pdb
• 関連するPDBエントリー: 8SQ9 8SQJ
• EMDBエントリー: 40699 40707 40708
• 分子名称: RNA-directed RNA polymerase nsp12, MAGNESIUM ION, Non-structural protein 8, ... (11 entities in total)
• 機能のキーワード: rtc, nsp12, nsp9, niran, sars-cov-2, dernaylation, mrna capping, umpcpp, viral protein
• 由来する生物種: Severe acute respiratory syndrome coronavirus 2; 詳細
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 200705.81

構造登録者

Small, G.I.,Darst, S.A.,Campbell, E.A. (登録日: 2023-05-04, 公開日: 2023-11-22, 最終更新日: 2025-05-21)

主引用文献

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

実験手法

ELECTRON MICROSCOPY (3.01 Å)