6W6O image
Entry Detail
PDB ID:
6W6O
EMDB ID:
Title:
NaChBac-Nav1.7VSDII chimera and HWTX-IV complex
Biological Source:
PDB Version:
Deposition Date:
2020-03-17
Release Date:
2020-06-24
Method Details:
Experimental Method:
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:NaChBac-Nav1.7VSDII chimera
Chain IDs:A, C (auth: D), E (auth: F), G (auth: H)
Chain Length:277
Number of Molecules:4
Biological Source:Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125), Homo sapiens
Polymer Type:polypeptide(L)
Description:Huwentoxin-IV
Chain IDs:B (auth: C), D (auth: E), F (auth: G), H (auth: I)
Chain Length:35
Number of Molecules:4
Biological Source:Cyriopagopus schmidti
Ligand Molecules
Primary Citation
Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na + channels in nanodisc.
Proc.Natl.Acad.Sci.USA 117 14187 14193 (2020)
PMID: 32513729 DOI: 10.1073/pnas.1922903117

Abstact

NaChBac, the first bacterial voltage-gated Na+ (Nav) channel to be characterized, has been the prokaryotic prototype for studying the structure-function relationship of Nav channels. Discovered nearly two decades ago, the structure of NaChBac has not been determined. Here we present the single particle electron cryomicroscopy (cryo-EM) analysis of NaChBac in both detergent micelles and nanodiscs. Under both conditions, the conformation of NaChBac is nearly identical to that of the potentially inactivated NavAb. Determining the structure of NaChBac in nanodiscs enabled us to examine gating modifier toxins (GMTs) of Nav channels in lipid bilayers. To study GMTs in mammalian Nav channels, we generated a chimera in which the extracellular fragment of the S3 and S4 segments in the second voltage-sensing domain from Nav1.7 replaced the corresponding sequence in NaChBac. Cryo-EM structures of the nanodisc-embedded chimera alone and in complex with HuwenToxin IV (HWTX-IV) were determined to 3.5 and 3.2 Å resolutions, respectively. Compared to the structure of HWTX-IV-bound human Nav1.7, which was obtained at an overall resolution of 3.2 Å, the local resolution of the toxin has been improved from ∼6 to ∼4 Å. This resolution enabled visualization of toxin docking. NaChBac can thus serve as a convenient surrogate for structural studies of the interactions between GMTs and Nav channels in a membrane environment.

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Primary Citation of related structures