7XU5

Structure of SARS-CoV-2 D614G Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Closed Conformation

7XU5 の概要

• エントリーDOI: 10.2210/pdb7xu5/pdb
• EMDBエントリー: 33453 33459
• 分子名称: Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, BILIVERDINE IX ALPHA, ... (4 entities in total)
• 機能のキーワード: protein engineering, spike protein, sars-cov-2, 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: 3
• 化学式量合計: 384938.22

構造登録者

Qu, K.,Chen, Q.,Ciazynska, K.A.,Liu, B.,Zhang, X.,Wang, J.,He, Y.,Guan, J.,He, J.,Liu, T.,Zhang, X.,Carter, A.P.,Xiong, X.,Briggs, J.A.G. (登録日: 2022-05-18, 公開日: 2022-07-20, 最終更新日: 2022-08-17)

主引用文献

Qu, K.,Chen, Q.,Ciazynska, K.A.,Liu, B.,Zhang, X.,Wang, J.,He, Y.,Guan, J.,He, J.,Liu, T.,Zhang, X.,Carter, A.P.,Xiong, X.,Briggs, J.A.G.
Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike.
Plos Pathog., 18:e1010583-e1010583, 2022

PubMed Abstract: The spike (S) protein of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the function of the locked conformation remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct "S-R/x3" to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures confirming that the x3 disulfide bond has the ability to stabilize the otherwise transient locked conformations. Structural analyses reveal that wild-type SARS-CoV-2 spike can adopt two distinct locked-1 and locked-2 conformations. For the D614G spike, based on which all variants of concern were evolved, only the locked-2 conformation was observed. Analysis of the structures suggests that rigidified domain D in the locked conformations interacts with the hinge to domain C and thereby restrains RBD movement. Structural change in domain D correlates with spike conformational change. We propose that the locked-1 and locked-2 conformations of S are present in the acidic high-lipid cellular compartments during virus assembly and egress. In this model, release of the virion into the neutral pH extracellular space would favour transition to the closed or open conformations. The dynamics of this transition can be altered by mutations that modulate domain D structure, as is the case for the D614G mutation, leading to changes in viral fitness. The S-R/x3 construct provides a tool for the further structural and functional characterization of the locked conformations of S, as well as how sequence changes might alter S assembly and regulation of receptor binding domain dynamics.

PubMed: 35905112
DOI: 10.1371/journal.ppat.1010583

実験手法

ELECTRON MICROSCOPY (3.1 Å)