9DBN image
Entry Detail
PDB ID:
9DBN
EMDB ID:
Title:
Tarantula venom peptide Protoxin-I bound to full-length human voltage-gated sodium channel 1.8 (NaV1.8)
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2024-08-23
Release Date:
2025-02-19
Method Details:
Experimental Method:
Resolution:
2.76 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Sodium channel protein type 10 subunit alpha
Chain IDs:A
Chain Length:2001
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Beta/omega-theraphotoxin-Tp1a
Chain IDs:B
Chain Length:35
Number of Molecules:1
Biological Source:Thrixopelma pruriens
Primary Citation
Structural basis of inhibition of human Na V 1.8 by the tarantula venom peptide Protoxin-I.
Nat Commun 16 1459 1459 (2025)
PMID: 39920100 DOI: 10.1038/s41467-024-55764-z

Abstact

Voltage-gated sodium channels (NaVs) selectively permit diffusion of sodium ions across the cell membrane and, in excitable cells, are responsible for propagating action potentials. One of the nine human NaV isoforms, NaV1.8, is a promising target for analgesics, and selective inhibitors are of interest as therapeutics. One such inhibitor, the gating-modifier peptide Protoxin-I derived from tarantula venom, blocks channel opening by shifting the activation voltage threshold to more depolarized potentials, but the structural basis for this inhibition has not previously been determined. Using monolayer graphene grids, we report the cryogenic electron microscopy structures of full-length human apo-NaV1.8 and the Protoxin-I-bound complex at 3.1 Å and 2.8 Å resolution, respectively. The apo structure shows an unexpected movement of the Domain I S4-S5 helix, and VSDI was unresolvable. We find that Protoxin-I binds to and displaces the VSDII S3-S4 linker, hindering translocation of the S4II helix during activation.

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Primary Citation of related structures