6VX3

NaChBac in GDN


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na+channels in nanodisc.

Gao, S.Valinsky, W.C.On, N.C.Houlihan, P.R.Qu, Q.Liu, L.Pan, X.Clapham, D.E.Yan, N.

(2020) Proc Natl Acad Sci U S A 117: 14187-14193

  • DOI: 10.1073/pnas.1922903117
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • NaChBac, the first bacterial voltage-gated Na + (Na v ) channel to be characterized, has been the prokaryotic prototype for studying the structure-function relationship of Na v channels. Discovered nearly two decade ...

    NaChBac, the first bacterial voltage-gated Na + (Na v ) channel to be characterized, has been the prokaryotic prototype for studying the structure-function relationship of Na v 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 Na v Ab. Determining the structure of NaChBac in nanodiscs enabled us to examine gating modifier toxins (GMTs) of Na v channels in lipid bilayers. To study GMTs in mammalian Na v channels, we generated a chimera in which the extracellular fragment of the S3 and S4 segments in the second voltage-sensing domain from Na v 1.7 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 Na v 1.7, 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 v channels in a membrane environment.


    Organizational Affiliation

    Department of Molecular Biology, Princeton University, Princeton, NJ 08544; nyan@princeton.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BH1501 protein
A, B, C, D
274Bacillus halodurans C-125Mutation(s): 0 
Gene Names: BH1501
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
NaChBac voltage-gated Na+ (NaV) channel in glyo-diosgenin (GDN) detergent
Find proteins for Q9KCR8 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Go to UniProtKB:  Q9KCR8
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download CCD File 
A, B, C, D
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-02-21 
  • Released Date: 2020-06-24 
  • Deposition Author(s): Yan, N., Gao, S.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDMR-1420541

Revision History 

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references