Voltage-gated ion channels confer excitability to biological membranes, initiating and propagating electrical signals across large distances on short timescales. Membrane excitation requires channels that respond to changes in electric field and couple the transmembrane voltage to gating of a central pore. To address the mechanism of this process in a voltage-gated ion channel, we determined structures of the plant two-pore channel 1 at different stages along its activation coordinate. These high-resolution structures of activation intermediates, when compared with the resting-state structure, portray a mechanism in which the voltage-sensing domain undergoes dilation and in-membrane plane rotation about the gating charge–bearing helix, followed by charge translocation across the charge transfer seal. These structures, in concert with patch-clamp electrophysiology, show that residues in the pore mouth sense inhibitory Ca
2+ and are allosterically coupled to the voltage sensor. These conformational changes provide insight into the mechanism of voltage-sensor domain activation in which activation occurs vectorially over a series of elementary steps.Voltage-gated ion channels (VGICs) use voltage-sensing domains (VSDs) to sense changes in electrical potential across biological membranes (
1,
2). VSDs are composed of a four-helix bundle, in which one helix carries charged residues that move in response to changes in transmembrane electric field (
3,
4). VSDs usually adopt a “resting state” when the membrane is at “resting potential”: ∼ −80 mV for animal and ∼ −150 mV for plant plasma membranes (
5). In comparison, much lower resting membrane voltages are set for intracellular endo-membranes: ∼ −30 mV across the plant vacuole (
6) and mammalian lysosome (
7). As the membrane potential vanishes during depolarization, so does the downward electrostatic force on the cationic side chains causing them to relax toward the outside of the membrane across a hydrophobic constriction site (HCS) or hydrophobic seal (
8). This conformational change is conveyed to the central pore, formed by four pore domains in a quasi-fourfold arrangement, which dilates to allow the diffusion of ions down their electrochemical gradients. The exact nature of the conformational change in VSDs has been the subject of decades of biophysical investigation (
9–
12), though to this date, only a few structural examples exist of voltage sensors in resting or multiple conformations (
13–
18).Two-pore channels (TPCs) are defined by their two tandem
Shaker-like cassette subunits in a single polypeptide chain, which dimerize to form a C2-symmetric channel with four subunits and 24 (4 × 6) transmembrane helices (
19–
21). There are three TPC channels, TPC1, 2, and 3, each with different voltage or ligand gating and ion selectivity. Among the voltage-gated TPCs (all except lipid-gated TPC2), only the second VSD (VSD2) is electrically active (
18,
22–
24), while VSD1 is insensitive to voltage changes and is likely static under all changes in potential.In plants, the vacuole comprises up to 90% of the plant cell volume and provides for a dynamic storage organelle that, in addition to metabolites, is a repository for ions including Ca
2+. TPC1 channels confer excitability to this intracellular organelle (
25) and, unlike other TPCs, are calcium regulated: external Ca
2+ (in the vacuolar lumen) inhibits the channel by binding to multiple luminal sites, while cytosolic Ca
2+ is required to open the channel by binding to EF hands, although the exact mechanism by which this activation occurs is unknown (
22). These electrical properties allowed our group and Youxing Jiang’s group to determine the first structure of an electrically resting VGIC by cocrystallizing the channel with 1 mM Ca
2+, which maintains the VSD in a resting configuration at 0 mV potential (
16,
22).Previously (
17), we used a gain-of-function mutant of AtTPC1 with three luminal Ca
2+-binding acidic residues on VSD2 neutralized (D240N/D454N/E528N) termed AtTPC1
DDE (abbreviated here as DDE) to visualize channel activation at the level of atomic structure, but we were unable to sufficiently resolve details of the electrically active VSD2 due to structural heterogeneity. In addition, the intracellular activation gate remained closed. We now present multiple structures of intermediately activated states of AtTPC1 determined by extensive image processing. In order to visualize such states, we modulated the channel’s luminal Ca
2+ sensitivity using a well-studied gain-of-function single-point mutant, D454N (
fou2), and also the triple mutant DDE for comparison.
fou2 is known to desensitize the channel to inhibitory, external (luminal) calcium ions (
26,
27). Mutations in D454 and closely related luminal Ca
2+-binding carboxyls to alanine D240A, D454A, E528A (termed AtTPC1ΔCa
i) were previously shown to effectively attenuate the Ca
2+-induced shift of the voltage activation threshold of AtTPC1 to depolarizing potentials at high luminal Ca
2+ (
28).The
fou2 and DDE mutations lie in the coordination sphere of the inhibitory Ca
2+ site on the luminal side of the VSD2–pore interface formed by D454, D240, and E528. The D454N mutation in the
fou2 channel enhances the defense capacity of plants against fungal or herbivore attack due to increased production of the wounding hormone jasmonate (
29). These effects on plant performance and defense are probably due to short circuiting of the vacuolar membrane (
26,
27,
30) in which TPC1 has increased open probability at resting potential. Compared to wild-type (WT) TPC1, the activation threshold in the
fou2 channel is shifted to more negatively polarized potentials and also has significantly lower sensitivity to inhibitory Ca
2+ in addition to exhibiting faster activation kinetics than its WT counterpart that was originally named the “slow vacuolar” (SV) channel due to its slow conductance onset (
20,
21,
30). Therefore, D454N confers more than just reduced sensitivity to external Ca
2+ but intrinsic hyperactivity as well. Our structures of these AtTPC1 mutants attempt to explain how the voltage sensor functions during electrical activation and how exactly luminal Ca
2+ affects this process.
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