Data export CSV files from HDX Workbench, software platform for the analysis of hydrogen/deuterium exchange (HDX) mass spectrometry data.

In enterobacteria such as Escherichia coli, the general stress response is mediatedby σs, the stationary phase dissociable promoter specificity subunit of RNApolymerase. σs is degraded by ClpXP during active growth in a process dependent onthe RssB adaptor, which is thought to be stimulated by phosphorylation of a conservedaspartate in its N-terminal receiver domain. Here we present the crystal structure offull-length RssB bound to a beryllofluoride phosphomimic. Compared to the structure ofRssB bound to the IraD anti-adaptor, our new RssB structure with bound beryllofluoridereveals conformational differences and coil-to-helix transitions in the C-terminal regionof the RssB receiver domain and in the inter-domain segmented helical linker. Theseare accompanied by masking of the α4-β5-α5 (4-5-5) “signaling” face of the RssBreceiver domain by its C-terminal domain. Critically, using hydrogen-deuteriumexchange mass spectrometry we identify σs binding determinants on the 4-5-5 face,implying that this surface needs to be unmasked to effect an interdomain interfaceswitch and enable full σs engagement and hand-off to ClpXP. In activated receiverdomains, the 4-5-5 face is often the locus of intermolecular interactions, but its maskingby intramolecular contacts upon phosphorylation is unusual, emphasizing that RssB isa response regulator that undergoes atypical regulation.Files included are data export from HDX Workbench software from the HDX-MS experiments in support of this work. The files are in CSV format.

在大肠杆菌（Escherichia coli）等肠杆菌科细菌中，整体应激反应由σs介导，后者是RNA聚合酶（RNA polymerase）的稳定期解离型启动子特异性亚基。在活跃生长阶段，σs会被ClpXP蛋白酶复合物降解，这一过程依赖于RssB适配蛋白（RssB）；此前研究认为，该过程可通过其N端接收结构域（N-terminal receiver domain）内一处保守天冬氨酸残基的磷酸化得到激活。本研究报道了结合氟化铍磷酸模拟物（beryllofluoride phosphomimic）的全长RssB晶体结构。与结合IraD抗适配蛋白（IraD anti-adaptor）的RssB结构相比，我们新解析的结合氟化铍的RssB结构显示，其接收结构域的C端区域以及域间分段螺旋连接区（inter-domain segmented helical linker）存在构象差异与无规卷曲向α螺旋的转变。伴随该构象变化的是，RssB接收结构域的α4-β5-α5（4-5-5）“信号面”被其C端结构域遮蔽。至关重要的是，本研究通过氢氘交换质谱（Hydrogen-Deuterium Exchange Mass Spectrometry, HDX-MS）鉴定出了4-5-5面上的σs结合决定簇，这表明该表面需要去遮蔽才能实现域间界面转换，进而完成σs的完全结合并将其递呈给ClpXP。在激活的接收结构域中，4-5-5面通常是分子间相互作用的位点，但该表面在磷酸化后通过分子内接触被遮蔽的情况并不常见，这凸显出RssB是一类存在非典型调控机制的反应调节蛋白（response regulator）。本数据集包含支持本研究的HDX-MS实验数据，均为HDX工作台软件（HDX Workbench）导出的逗号分隔值（CSV）格式文件。