9VCL

Cryo-EM structure of SARS-CoV-2 nsp10/nsp14:RNA:ATMP complex

9VCL の概要

• エントリーDOI: 10.2210/pdb9vcl/pdb
• EMDBエントリー: 64957
• 分子名称: Non-structural protein 10, Guanine-N7 methyltransferase nsp14, RNA (26-MER), ... (8 entities in total)
• 機能のキーワード: sars-cov-2, exonuclease, nsp14, nucleotide analogue, viral protein/rna, viral protein-rna complex
• 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: 4
• 化学式量合計: 92662.10

構造登録者

Wang, J.,Lou, Z.,Liu, D. (登録日: 2025-06-06, 公開日: 2025-07-16)

主引用文献

Wang, J.,Pan, Y.,Liu, Y.,Huang, B.,Jin, G.,Zhang, L.,Zhou, F.,Chang, X.,Huang, Y.,Yan, L.,Dong, Y.,Rao, Z.,Liu, D.,Lou, Z.
Structural Basis and Rational Design of Nucleotide Analogue Inhibitor Evading the SARS-CoV-2 Proofreading Enzyme.
J.Am.Chem.Soc., 147:21896-21906, 2025

PubMed Abstract: All coronaviruses (CoVs) encode an exoribonuclease in nonstructural protein nsp14 (nsp14 ExoN), which is required for the excision of mismatched nucleotides or nucleotide analogues (NAs) that are incorporated into nascent RNA. Here, we investigated the mechanism by which NAs evade SARS-CoV-2 nsp14 ExoN cleavage using chemically synthesized RNA with NAs incorporated at the 3' end. Nsp14 ExoN exhibited significantly attenuated activity on RNA with sofosbuvir monophosphate (SMP) compared with natural nucleotides, remdesivir/molnupiravir monophosphate, and, in particular, AT-9010 monophosphate (ATMP), which has the same chemically modified ribose moiety as SMP, incorporated at the 3' end. Cryo-electron microscopy structures of nsp10/14 bound to RNA-SMP/-ATMP and mutagenesis studies revealed the essential roles of H95/Q145/F146 in recognizing the base moiety and thus pulling the NAs into a favored conformation for cleavage. Therefore, NAs may evade nsp14 ExoN cleavage by having (1) a base that does not interact with H95, Q145, or F146 and (2) a chemically modified ribose. Guided by this hypothesis, two NAs were designed to effectively resist nsp14 ExoN cleavage. These results inform the rational design of anti-CoV NAs.

PubMed: 40509573
DOI: 10.1021/jacs.5c05014

実験手法

ELECTRON MICROSCOPY (3.08 Å)