Structural characterization of pH- and calcium-modulated open and closed states of the pentameric ligand-gated ion channel DeCLIC

Pentameric ligand-gated ion channels are critical mediators of electrochemical signal transduction in a variety of excitable cells. Biophysical and pharmacological development in this family relies heavily on high-quality structural data in multiple distinct functional states. Bacterial pLGICs can provide valuable insight into fundamental mechanisms of gating, as they often desensitize to a lesser extent than eukaryotic channels, while retaining sensitivity to modulatory conditions such as pH and environmental calcium. Recently, a new prokaryotic family member (DeCLIC) from a Desulfofustis deltaproteobacterium was identified, including a previously uncharacterized N-terminal domain. The channel was found to be modulated by calcium ions, and with Ca2+ present it crystallized with a dramatically expanded pore. Here, we used cryo-electron microscopy to identify multiple conformations of the channel under acidic conditions. When Ca2+ was present, two classes of particles of roughly equal proportion were identified, one class was similar to the crystallographic closed state, while the second class represented an apparent open state notably divergent from the open X-ray structure. When Ca2+ was absent, the predominant class had a similar open pore, while a second class had a closed pore and evidence for a highly dynamic N-terminal domain. These data provide new insight into pH modulation and the under-characterized open state of pentameric channels, as well as a novel mechanism of dynamic ion-channel regulation via an N-terminal module.