Structural Superimposition

Abstact

Voltage-gated sodium (Na(v)) channels are key targets of various venomous toxins. Deciphering the binding poses and mechanisms of action of representative toxins will help to dissect the functional mechanism of the channels and facilitate therapeutic development targeting Na(v) channels(1,2). Here we present cryo-electron microscopy (cryo-EM) structures of distinct binding poses of three agonistic peptide toxins on the human Na(v)1.6-beta1 channel complex. The globular beta-scorpion toxin Cn2 nestles between the extracellular segment of voltage-sensing domain (VSD) in the second repeat of the Na(v)1.6 core alpha-unit (VSD(II)) and the pore extracellular loops in the third repeat of the Na(v)1.6 core alpha-unit (ECL(III)), where it is stabilized by interactions with both protein regions and the branched N1372-glycan. Cone snail iota-conotoxin RXIA adopts an elongated conformation, spanning VSD(I) and VSD(IV) to wrap around the shoulder of the pore domain (PD). The bullet ant-derived toxin delta-paraponeritoxin-Pc1a exists as a transmembrane helix that stands between VSD(II) and PD(III). Our findings, corroborated by functional characterizations, illustrate the diversity in peptide toxin binding poses and mechanisms of action, link stabilization of the up state of VSD(I) or VSD(II) to channel activation, and provide clues to the rational design of selective Na(v) channel modulators.