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- EMDB-6770: Structure of the Nav1.4-beta1 complex from electric eel -

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Basic information

Entry
Database: EMDB / ID: 6770
TitleStructure of the Nav1.4-beta1 complex from electric eel
Map dataexperimental map
Samplevoltage gated sodium channel EeNav1.4
  • Sodium channel protein
  • Voltage-gated sodium channel beta subunit 1
  • (ligand) x 2
Function / homologyImmunoglobulin V-set domain / Voltage-dependent channel domain superfamily / Ig-like domain profile. / Immunoglobulin V-set domain / Sodium ion transport-associated / Ion transport protein / Voltage gated sodium channel, alpha subunit / Ion transport domain / Immunoglobulin-like domain / Sodium ion transport-associated ...Immunoglobulin V-set domain / Voltage-dependent channel domain superfamily / Ig-like domain profile. / Immunoglobulin V-set domain / Sodium ion transport-associated / Ion transport protein / Voltage gated sodium channel, alpha subunit / Ion transport domain / Immunoglobulin-like domain / Sodium ion transport-associated / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Sodium channel subunit beta-1/beta-3 / voltage-gated sodium channel complex / voltage-gated sodium channel activity / voltage-gated ion channel activity / sodium ion transport / regulation of ion transmembrane transport / sodium channel regulator activity / Voltage-gated sodium channel beta subunit 1 / Sodium channel protein
Function and homology information
SourceElectrophorus electricus (electric eel)
Methodsingle particle reconstruction / cryo EM / 4 Å resolution
AuthorsYan Z / Zhou Q
CitationJournal: Cell / Year: 2017
Title: Structure of the Na1.4-β1 Complex from Electric Eel.
Authors: Zhen Yan / Qiang Zhou / Lin Wang / Jianping Wu / Yanyu Zhao / Gaoxingyu Huang / Wei Peng / Huaizong Shen / Jianlin Lei / Nieng Yan
Abstract: Voltage-gated sodium (Na) channels initiate and propagate action potentials. Here, we present the cryo-EM structure of EeNa1.4, the Na channel from electric eel, in complex with the β1 subunit at 4. ...Voltage-gated sodium (Na) channels initiate and propagate action potentials. Here, we present the cryo-EM structure of EeNa1.4, the Na channel from electric eel, in complex with the β1 subunit at 4.0 Å resolution. The immunoglobulin domain of β1 docks onto the extracellular L5 and L6 loops of EeNa1.4 via extensive polar interactions, and the single transmembrane helix interacts with the third voltage-sensing domain (VSD). The VSDs exhibit "up" conformations, while the intracellular gate of the pore domain is kept open by a digitonin-like molecule. Structural comparison with closed NaPaS shows that the outward transfer of gating charges is coupled to the iris-like pore domain dilation through intricate force transmissions involving multiple channel segments. The IFM fast inactivation motif on the III-IV linker is plugged into the corner enclosed by the outer S4-S5 and inner S6 segments in repeats III and IV, suggesting a potential allosteric blocking mechanism for fast inactivation.
Validation ReportPDB-ID: 5xsy

SummaryFull reportAbout validation report
DateDeposition: Jun 15, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Aug 9, 2017 / Last update: Aug 9, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5xsy
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6770.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.34 Å/pix.
= 267.6 Å
200 pix
1.34 Å/pix.
= 267.6 Å
200 pix
1.34 Å/pix.
= 267.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.338 Å
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.22568451 - 0.33369038
Average (Standard dev.)0.0012356095 (0.013148039)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 267.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3381.3381.338
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z267.600267.600267.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.2260.3340.001

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Supplemental data

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Sample components

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Entire voltage gated sodium channel EeNav1.4

EntireName: voltage gated sodium channel EeNav1.4 / Number of components: 5

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Component #1: cellular-component, voltage gated sodium channel EeNav1.4

Cellular-componentName: voltage gated sodium channel EeNav1.4 / Recombinant expression: No
SourceSpecies: Electrophorus electricus (electric eel)

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Component #2: protein, Sodium channel protein

ProteinName: Sodium channel protein / Recombinant expression: No
MassTheoretical: 208.519797 kDa
SourceSpecies: Electrophorus electricus (electric eel)

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Component #3: protein, Voltage-gated sodium channel beta subunit 1

ProteinName: Voltage-gated sodium channel beta subunit 1 / Recombinant expression: No
MassTheoretical: 23.657322 kDa
SourceSpecies: Electrophorus electricus (electric eel)

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Component #4: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #5: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 123431
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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