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Structure paper

TitleDiverse binding poses of agonistic neurotoxins on human Na1.6.
Journal, issue, pagesNature, Year 2026
Publish dateJun 10, 2026
AuthorsXiao Fan / Jian Huang / Lin Yang / Jiaofeng Chen / Huan Wang / Xiaoshuang Huang / Jinli Geng / Qinglin Wu / Yuzhen Xie / Fangzhou Lu / Qinmeng Guo / Zilin Shen / Xueqin Jin / Nieng Yan /
PubMed AbstractVoltage-gated sodium (Na) 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 ...Voltage-gated sodium (Na) 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 channels. Here we present cryo-electron microscopy (cryo-EM) structures of distinct binding poses of three agonistic peptide toxins on the human Na1.6-β1 channel complex. The globular β-scorpion toxin Cn2 nestles between the extracellular segment of voltage-sensing domain (VSD) in the second repeat of the Na1.6 core α-unit (VSD) and the pore extracellular loops in the third repeat of the Na1.6 core α-unit (ECL), where it is stabilized by interactions with both protein regions and the branched N1372-glycan. Cone snail ι-conotoxin RXIA adopts an elongated conformation, spanning VSD and VSD to wrap around the shoulder of the pore domain (PD). The bullet ant-derived toxin δ-paraponeritoxin-Pc1a exists as a transmembrane helix that stands between VSD and PD. 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 or VSD to channel activation, and provide clues to the rational design of selective Na channel modulators.
External linksNature / PubMed:42271061
MethodsEM (single particle)
Resolution2.5 - 3.1 Å
Structure data

80133

25ih

EMDB-80133, PDB-25ih:
Cryo-EM structure of human Nav1.6 in complex with Cn2
Method: EM (single particle) / Resolution: 2.8 Å

80134

25ii

EMDB-80134, PDB-25ii:
Cryo-EM structure of human Nav1.6 in complex with Iota-Conotoxin RXIA
Method: EM (single particle) / Resolution: 2.5 Å

80135

25ij

EMDB-80135, PDB-25ij:
Cryo-EM structure of human Nav1.6 in complex with delta-paraponeritoxin-Pc1a
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-9Z9:
(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en / detergent*YM

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

ChemComp-CLR:
CHOLESTEROL

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

ChemComp-LPE:
1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

ChemComp-P3X:
(5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosphatricos-5-en-17-yl hexadecanoate

ChemComp-PT5:
[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho / phospholipid*YM

ChemComp-HOH:
WATER

ChemComp-NA:
Unknown entry

Source
  • homo sapiens (human)
  • centruroides noxius (Mexican scorpion)
  • conus radiatus (invertebrata)
  • paraponera clavata (insect)
KeywordsMEMBRANE PROTEIN / Nav1.6 / voltage gated sodium channel / cryo-EM / toxin / Cn2 / TRANSPORT PROTEIN-TOXIN complex / Iota-Conotoxin RXIA / Pc1a / delta-paraponeritoxin-Pc1a / TRANSPORT PROTEIN

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