SARS-CoV-2 ORF3a is believed to form ion channels, which may be involved in the modulation of virus release, and has been implicated in various cellular processes like the up-regulation of fibrinogen expression in lung epithelial cells, downregulation of type 1 interferon receptor, caspase-dependent apoptosis, and increasing IFNAR1 ubiquitination. ORF3a assemblies as homotetramers, which are stabilized by residue C133. A recent cryoEM structure of a homodimeric complex of ORF3a has been released. A lower-resolution cryoEM map of the tetramer suggests two dimers form it, arranged side by side. The dimer's cryoEM structure revealed that each protomer contains three transmembrane helices arranged in a clockwise configuration forming a six helices transmembrane domain. This domain's potential permeation pathway has six constrictions narrowing to about 0.1 nm in radius, suggesting the structure solved is in a closed or inactivated state. At the cytosol end, the permeation pathway encounters a large and polar cavity formed by multiple beta strands from both protomers, which opens to the cytosolic milieu. We modeled the tetramer following the arrangement suggested by the low-resolution tetramer cryoEM map. Molecular dynamics simulations of the tetramer embedded in a membrane and solvated with 0.5 M of KCl were performed. Our simulations show the cytosolic cavity is quickly populated by both K+ and Cl-, yet with different dynamics. K+ ions moved relatively free inside the cavity without forming proper coordination sites. In contrast, Cl- ions enter the cavity, and three of them can become stably coordinated near the intracellular entrance of the potential permeation pathway by an inter-subunit network of positively charged amino acids. Consequently, the central cavity's electrostatic potential changed from being entirely positive at the beginning of the simulation to more electronegative at the end.

中文翻译：

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对SARS-CoV-2 ORF3a结构的分析揭示了氯化物结合位点

SARS-CoV-2 ORF3a被认为可形成离子通道，可能参与病毒释放的调节，并已参与多种细胞过程，例如肺上皮细胞中纤维蛋白原表达的上调，1型干扰素的下调。受体，caspase依赖性细胞凋亡和IFNAR1泛素化增加。ORF3a组装为同四聚体，由残基C133稳定。ORF3a同型二聚体复合物的最新cryoEM结构已经发布。较低分辨率的cryoEM图谱显示四聚体由两个二聚体形成，并排排列。二聚体的cryoEM结构表明，每个protomer包含三个跨膜螺旋，它们按顺时针方向排列，形成六个螺旋跨膜结构域。这个网域 潜在的渗透途径有六个缩窄至半径约0.1 nm的缩颈，表明所解决的结构处于封闭或失活状态。在细胞质末端，渗透途径遇到了一个大的极性空腔，该空腔由来自两个前体的多个β链形成，并向胞质环境开放。我们按照低分辨率四聚体cryoEM图建议的排列对四聚体建模。进行了嵌入膜中并用0.5 M KCl溶剂化的四聚体的分子动力学模拟。我们的模拟显示，胞质腔被K +和Cl-迅速填充，但动力学却不同。K +离子在腔体内相对自由地移动，而没有形成适当的配位点。相反，Cl-离子进入空腔，它们中的三个可以通过带正电荷的氨基酸的亚基间网络在潜在的渗透途径的细胞内入口附近稳定地协调。因此，中心腔的静电势从模拟开始时的完全正变为结束时的更大的负电。