8V8E

Room-temperature X-ray structure of SARS-CoV-2 main protease catalytic domain (residues 1-199-6H) in complex with ensitrelvir (ESV)

8V8E の概要

• エントリーDOI: 10.2210/pdb8v8e/pdb
• 関連するPDBエントリー: 8V7T 8V7W
• 分子名称: 3C-like proteinase nsp5, peptide, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione, ... (4 entities in total)
• 機能のキーワード: inhibitor complex, catalytic domain, cysteine protease, hydrolase
• 由来する生物種: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 48032.05

構造登録者

Kovalevsky, A.,Coates, L. (登録日: 2023-12-05, 公開日: 2024-05-29, 最終更新日: 2024-06-12)

主引用文献

Kovalevsky, A.,Aniana, A.,Coates, L.,Ghirlando, R.,Nashed, N.T.,Louis, J.M.
Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease.
J.Mol.Biol., 436:168616-168616, 2024

PubMed Abstract: N-terminal autoprocessing from its polyprotein precursor enables creating the mature-like stable dimer interface of SARS-CoV-2 main protease (MPro), concomitant with the active site oxyanion loop equilibrium transitioning to the active conformation (E*) and onset of catalytic activity. Through mutagenesis of critical interface residues and evaluating noncovalent inhibitor (ensitrelvir, ESV) facilitated dimerization through its binding to MPro, we demonstrate that residues extending from Ser1 through Glu14 are critical for dimerization. Combined mutations G11A, E290A and R298A (MPro™) restrict dimerization even upon binding of ESV to monomeric MPro™ with an inhibitor dissociation constant of 7.4 ± 1.6 µM. Contrasting the covalent inhibitor NMV or GC373 binding to monomeric MPro, ESV binding enabled capturing the transition of the oxyanion loop conformations in the absence of a reactive warhead and independent of dimerization. Characterization of complexes by room-temperature X-ray crystallography reveals ESV bound to the E* state of monomeric MPro as well as an intermediate approaching the inactive state (E). It appears that the E* to E equilibrium shift occurs initially from G138-F140 residues, leading to the unwinding of the loop and formation of the 3-helix. Finally, we describe a transient dimer structure of the MPro precursor held together through interactions of residues A5-G11 with distinct states of the active sites, E and E*, likely representing an intermediate in the autoprocessing pathway.

PubMed: 38762033
DOI: 10.1016/j.jmb.2024.168616

実験手法

X-RAY DIFFRACTION (2 Å)