Structural basis for voltage-sensor trapping of the cardiac sodium channel by a deathstalker scorpion toxin

Abstract

Voltage-gated sodium (NaV) channels initiate action potentials in excitable cells, and their function is altered by potent gating-modifier toxins. The α-toxin LqhIII from the deathstalker scorpion inhibits fast inactivation of cardiac NaV1.5 channels with IC50 = 11.4 nM. Here we reveal the structure of LqhIII bound to NaV1.5 at 3.3 Å resolution by cryo-EM. LqhIII anchors on top of voltage-sensing domain IV, wedged between the S1-S2 and S3-S4 linkers, which traps the gating charges of the S4 segment in a unique intermediate-activated state stabilized by four ion-pairs. This conformational change is propagated inward to weaken binding of the fast inactivation gate and favor opening the activation gate. However, these changes do not permit Na+ permeation, revealing why LqhIII slows inactivation of NaV channels but does not open them. Our results provide important insights into the structural basis for gating-modifier toxin binding, voltage-sensor trapping, and fast inactivation of NaV channels.

Mapping the interaction surface of scorpion β-toxins with an insect sodium channel

“…F48 between two beta-strands in Dc1a also penetrates deeply into chimeric channel in the apo-and AaH2-bound states [22] shows that major changes upon toxin binding occur in loop IVS3-S4, which forms multiple stabilizing contacts with the toxin. A dramatic toxin-induced shift of linker IVS3-S4 is also seen in the superimposed cryo-EM structures of rNav1.5 and its complex with the deathstalker scorpion toxin [23]. In agreement with the experimental structures, our BgNav1-1a-Lqh-dprIT3-c models with the activated and in-silico deactivated VSD-II also show large shift of IIS3-S4, which affect its contacts with the toxin (Fig.…”

“…Cryo-EM structures of several eukaryotic channels in the apo form and in complex with different toxins are now available, e.g., [20][21][22][23][24]. Although these structures are useful in rationalizing numerous mutational and ligand-binding studies, including action of chemical insecticides like pyrethroids and proteinaceous toxins, they are of limited resolution and represent snapshots of certain conformations captured in channel states with presumably inactivated pore domain [25].…”

Computational Analysis of the Crystal and Cryo-EM Structures of P-Loop Channels with Drugs

“…In the hNav1.4 channel [ 19 ], π-bulges significantly reorient residues in the C-terminal parts of helices IS6 and IIIS6 (PDB ID: 6agf). The same pattern of π-bulges in IS6 and IIIS6 is seen in hNav1.2 (PDB ID: 6j8e) [ 20 ], hNav1.7 (PDB ID: 6j8i) [ 21 ], and rNav1.5 (PDB IDs: 6uz3, 6uz0, 7k18) [ 22 , 23 ]. Figure 5 A shows that CA-CB bonds of conserved asparagines in position i20 form two distinct clusters depending on the presence or absence of π-bulges.…”

An open state of a voltage-gated sodium channel involving a π-helix and conserved pore-facing Asparagine

“…The mutation of this Asn to Asp in NaChBac leads to enhanced inactivation, while the mutation to any other residue is non-functional (86). In eukaryotic channels, the conserved Asn itself has been implicated in inactivation of Nav1.4 and Nav1.2a (79,87), and a direct interaction between the Asn on DIV-S6 (facing away from the pore lumen) and the IFM particle responsible for fast inactivation is found in structures of eukaryotic Nav channels solved in inactivated states (3,4,7,8). Of particular note, in all these structures, the S6 helix of DIV is systematically ɑ-helical while the S6 of the other domains may feature h-bonding defects and formation of p-helix segments coupled to the orientation of the conserved Asn into the pore domain (Figure 4.D,F).…”

“…(Figure 4.C). Indeed, the equivalent asparagine has also been shown to mediate coupling between the VSD and pore domain in the eukaryotic channels Nav1.4 and Nav1.5 (64) and to come in contact with the inactivation Ile-Phe-Met (IFM) particle of the channels solved in an inactivated state (3,4,7,8).…”