8EYJ

Crystal Structure of uncleaved SARS-CoV-2 Main Protease C145S mutant in complex with Nirmatrelvir

「8DG3」から置き換えられました

8EYJ の概要

• エントリーDOI: 10.2210/pdb8eyj/pdb
• 分子名称: 3C-like proteinase nsp5, (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide (3 entities in total)
• 機能のキーワード: main protease, complex, nirmatrelvir, viral protein
• 由来する生物種: Severe acute respiratory syndrome coronavirus 2
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 68878.30

構造登録者

Noske, G.D.,Godoy, A.S.,Oliva, G. (登録日: 2022-10-27, 公開日: 2022-11-16, 最終更新日: 2024-10-16)

主引用文献

Noske, G.D.,Song, Y.,Fernandes, R.S.,Chalk, R.,Elmassoudi, H.,Koekemoer, L.,Owen, C.D.,El-Baba, T.J.,Robinson, C.V.,Oliva, G.,Godoy, A.S.
An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition.
Nat Commun, 14:1545-1545, 2023

PubMed Abstract: The main protease from SARS-CoV-2 (M) is responsible for cleavage of the viral polyprotein. M self-processing is called maturation, and it is crucial for enzyme dimerization and activity. Here we use C145S M to study the structure and dynamics of N-terminal cleavage in solution. Native mass spectroscopy analysis shows that mixed oligomeric states are composed of cleaved and uncleaved particles, indicating that N-terminal processing is not critical for dimerization. A 3.5 Å cryo-EM structure provides details of M N-terminal cleavage outside the constrains of crystal environment. We show that different classes of inhibitors shift the balance between oligomeric states. While non-covalent inhibitor MAT-POS-e194df51-1 prevents dimerization, the covalent inhibitor nirmatrelvir induces the conversion of monomers into dimers, even with intact N-termini. Our data indicates that the M dimerization is triggered by induced fit due to covalent linkage during substrate processing rather than the N-terminal processing.

PubMed: 36941262
DOI: 10.1038/s41467-023-37035-5

実験手法

X-RAY DIFFRACTION (1.738 Å)