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- EMDB-2347: cryo-EM structure of the NavCt voltage-gated sodium channel -

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Basic information

Entry
Database: EMDB / ID: EMD-2347
Titlecryo-EM structure of the NavCt voltage-gated sodium channel
Map dataCryo-EM structure of voltage-gated Na+ channel
Sample
  • Sample: voltage-gated sodium channelSodium channel
  • Protein or peptide: voltage-gated sodium channelSodium channel
KeywordsVoltage-gated sodium ion channel / tetrameric ion channel
Function / homologyVoltage-dependent channel domain superfamily / Ion transport domain / Ion transport domain / Ion transport protein / monoatomic ion channel activity / membrane / Ion transport protein
Function and homology information
Biological speciesCaldalkalibacillus thermarum (bacteria)
Methodelectron crystallography / cryo EM / Resolution: 9.0 Å
AuthorsTsai C-J / Tani K / Irie K / Hiroaki Y / Shimomura T / McMillan DG / Cook GM / Schertler G / Fujiyoshi Y / Li X-D
CitationJournal: J Mol Biol / Year: 2013
Title: Two alternative conformations of a voltage-gated sodium channel.
Authors: Ching-Ju Tsai / Kazutoshi Tani / Katsumasa Irie / Yoko Hiroaki / Takushi Shimomura / Duncan G McMillan / Gregory M Cook / Gebhard F X Schertler / Yoshinori Fujiyoshi / Xiao-Dan Li /
Abstract: Activation and inactivation of voltage-gated sodium channels (Navs) are well studied, yet the molecular mechanisms governing channel gating in the membrane remain unknown. We present two ...Activation and inactivation of voltage-gated sodium channels (Navs) are well studied, yet the molecular mechanisms governing channel gating in the membrane remain unknown. We present two conformations of a Nav from Caldalkalibacillus thermarum reconstituted into lipid bilayers in one crystal at 9Å resolution based on electron crystallography. Despite a voltage sensor arrangement identical with that in the activated form, we observed two distinct pore domain structures: a prominent form with a relatively open inner gate and a closed inner-gate conformation similar to the first prokaryotic Nav structure. Structural differences, together with mutational and electrophysiological analyses, indicated that widening of the inner gate was dependent on interactions among the S4-S5 linker, the N-terminal part of S5 and its adjoining part in S6, and on interhelical repulsion by a negatively charged C-terminal region subsequent to S6. Our findings suggest that these specific interactions result in two conformational structures.
History
DepositionMar 28, 2013-
Header (metadata) releaseApr 10, 2013-
Map releaseJul 10, 2013-
UpdateNov 6, 2013-
Current statusNov 6, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4bgn
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4bgn
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2347.jpg

Downloads & links

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Map

FileDownload / File: emd_2347.map.gz / Format: CCP4 / Size: 936.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of voltage-gated Na+ channel
Voxel sizeX: 2.09091 Å / Y: 2.09091 Å / Z: 2.22222 Å
Density
Contour LevelBy EMDB: 1.3 / Movie #1: 1.3
Minimum - Maximum-5.02710009 - 6.8197999
Average (Standard dev.)0.00326918 (±0.99271661)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin00-40
Dimensions555581
Spacing555581
CellA: 115.0 Å / B: 115.0 Å / C: 180.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.09090909090912.09090909090912.2222222222222
M x/y/z555581
origin x/y/z0.0000.0000.000
length x/y/z115.000115.000180.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S213
start NC/NR/NS00-40
NC/NR/NS555581
D min/max/mean-5.0276.8200.003

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Supplemental data

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Sample components

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Entire : voltage-gated sodium channel

EntireName: voltage-gated sodium channelSodium channel
Components
  • Sample: voltage-gated sodium channelSodium channel
  • Protein or peptide: voltage-gated sodium channelSodium channel

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Supramolecule #1000: voltage-gated sodium channel

SupramoleculeName: voltage-gated sodium channel / type: sample / ID: 1000
Oligomeric state: Two tetramers of voltage-gated sodium channel
Number unique components: 1

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Macromolecule #1: voltage-gated sodium channel

MacromoleculeName: voltage-gated sodium channel / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Oligomeric state: tetramer / Recombinant expression: Yes
Source (natural)Organism: Caldalkalibacillus thermarum (bacteria) / Strain: TA2.A1 / Location in cell: Plasma membrane
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: C43 / Recombinant plasmid: pTrc99A
SequenceUniProtKB: Ion transport protein / GO: monoatomic ion channel activity / InterPro: Ion transport domain

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

Concentration4.0 mg/mL
BufferpH: 9
Details: 50mM glycine-NaOH pH9.0, 200mM NaCl, 4mM MgCl2, 5% glycerol, 5% methyl-2,4-pentanediol, 1.5mM NaN3
GridDetails: molybdenum EM grid
VitrificationCryogen name: NITROGEN / Instrument: LEICA KF80
DetailsCrystals grown by dialysis
Crystal formationDetails: Crystals grown by dialysis

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Electron microscopy

MicroscopeJEOL KYOTO-3000SFF
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.6 mm / Nominal defocus max: 3.82 µm / Nominal defocus min: 0.91 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Helium cooled, top entry / Specimen holder model: JEOL / Tilt angle max: 60 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 60 °
TemperatureMin: 4 K / Average: 4 K
DateNov 5, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 77 / Average electron dose: 20 e/Å2 / Bits/pixel: 14
Tilt angle min0

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Image processing

Crystal parametersUnit cell - A: 115.0 Å / Unit cell - B: 115.0 Å / Unit cell - C: 180.0 Å / Unit cell - γ: 90.0 ° / Unit cell - α: 90.0 ° / Unit cell - β: 90.0 ° / Plane group: P 4
CTF correctionDetails: Each micrographs
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: MRC
DetailsImages were processed using MRC suite

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Atomic model buiding 1

Initial modelPDB ID:

3rvy

SoftwareName: CNS
RefinementSpace: REAL
Output model

PDB-4bgn:
cryo-EM structure of the NavCt voltage-gated sodium channel

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