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TitleEmploying NaChBac for cryo-EM analysis of toxin action on voltage-gated Na channels in nanodisc.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 117, Issue 25, Page 14187-14193, Year 2020
Publish dateJun 23, 2020
AuthorsShuai Gao / William C Valinsky / Nguyen Cam On / Patrick R Houlihan / Qian Qu / Lei Liu / Xiaojing Pan / David E Clapham / Nieng Yan /
PubMed AbstractNaChBac, the first bacterial voltage-gated Na (Na) channel to be characterized, has been the prokaryotic prototype for studying the structure-function relationship of Na channels. Discovered nearly ...NaChBac, the first bacterial voltage-gated Na (Na) channel to be characterized, has been the prokaryotic prototype for studying the structure-function relationship of Na 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 NaAb. Determining the structure of NaChBac in nanodiscs enabled us to examine gating modifier toxins (GMTs) of Na channels in lipid bilayers. To study GMTs in mammalian Na channels, we generated a chimera in which the extracellular fragment of the S3 and S4 segments in the second voltage-sensing domain from Na1.7 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 Na1.7, 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 Na channels in a membrane environment.
External linksProc Natl Acad Sci U S A / PubMed:32513729 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 3.7 Å
Structure data

21425

6vwx

EMDB-21425, PDB-6vwx:
NaChBac in lipid nanodisc
Method: EM (single particle) / Resolution: 3.1 Å

21428

6vx3

EMDB-21428, PDB-6vx3:
NaChBac in GDN
Method: EM (single particle) / Resolution: 3.7 Å

21446

6vxo

EMDB-21446, PDB-6vxo:
NaChBac-Nav1.7VSDII chimera in nanodisc
Method: EM (single particle) / Resolution: 3.5 Å

21560

6w6o

EMDB-21560, PDB-6w6o:
NaChBac-Nav1.7VSDII chimera and HWTX-IV complex
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM / POPC

ChemComp-NA:
Unknown entry

Source
  • bacillus halodurans c-125 (bacteria)
  • bacillus halodurans (strain atcc baa-125 / dsm 18197 / ferm 7344 / jcm 9153 / c-125) (bacteria)
  • cyriopagopus schmidti (Chinese earth tiger)
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / NaChBac / Channels; Sodium Ion-Selective / TRANSPORT PROTEIN/TOXIN / Channels / Sodium Ion-Selective / TRANSPORT PROTEIN-TOXIN complex

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