+Open data
-Basic information
Entry | Database: PDB / ID: 6vxo | ||||||
---|---|---|---|---|---|---|---|
Title | NaChBac-Nav1.7VSDII chimera in nanodisc | ||||||
Components | NaChBac-Nav1.7VSDII chimera | ||||||
Keywords | MEMBRANE PROTEIN / NaChBac / Channels / Sodium Ion-Selective | ||||||
Function / homology | Function and homology information detection of mechanical stimulus involved in sensory perception / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / behavioral response to pain / Phase 0 - rapid depolarisation / detection of temperature stimulus involved in sensory perception of pain / sodium ion transmembrane transport ...detection of mechanical stimulus involved in sensory perception / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / behavioral response to pain / Phase 0 - rapid depolarisation / detection of temperature stimulus involved in sensory perception of pain / sodium ion transmembrane transport / monoatomic cation channel activity / sensory perception of pain / post-embryonic development / response to toxic substance / Sensory perception of sweet, bitter, and umami (glutamate) taste / circadian rhythm / inflammatory response / axon / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus halodurans C-125 (bacteria) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Yan, N. / Gao, S. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na channels in nanodisc. Authors: Shuai Gao / William C Valinsky / Nguyen Cam On / Patrick R Houlihan / Qian Qu / Lei Liu / Xiaojing Pan / David E Clapham / Nieng Yan / Abstract: 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 ...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. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6vxo.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vxo.ent.gz | 150 KB | Display | PDB format |
PDBx/mmJSON format | 6vxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vxo_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6vxo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6vxo_validation.xml.gz | 42 KB | Display | |
Data in CIF | 6vxo_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/6vxo ftp://data.pdbj.org/pub/pdb/validation_reports/vx/6vxo | HTTPS FTP |
-Related structure data
Related structure data | 21446MC 6vwxC 6vx3C 6w6oC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 31901.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans C-125 (bacteria), (gene. exp.) Homo sapiens (human) Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125 Gene: BH1501, SCN9A, NENA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KCR8, UniProt: Q15858 #2: Chemical | ChemComp-POV / ( Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NaChBac-Nav1.7VSDII chimera / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) | Organism: Bacillus halodurans C-125 (bacteria) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
| |||||||||||||||
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: NaChBac-Nav1.7VSDII chimera in lipid nanodisc | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: blot for 5 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 53 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17rc2_3619: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31147 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|