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- EMDB-6698: Structure of a eukaryotic voltage-gated sodium channel at near at... -

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Database: EMDB / ID: 6698
TitleStructure of a eukaryotic voltage-gated sodium channel at near atomic resolution
Samplevoltage-gated sodium channel
SourcePeriplaneta americana / arthropod / ワモンゴキブリ
Map dataoverall map
Methodsingle particle reconstruction, at 3.8 Å resolution
AuthorsShen H / Zhou Q
CitationScience, 2017, 355

Science, 2017, 355 Yorodumi Papers
Structure of a eukaryotic voltage-gated sodium channel at near-atomic resolution.
Huaizong Shen / Qiang Zhou / Xiaojing Pan / Zhangqiang Li / Jianping Wu / Nieng Yan

Validation ReportPDB-ID: 5x0m

SummaryFull reportAbout validation report
DateDeposition: Jan 21, 2017 / Header (metadata) release: Feb 15, 2017 / Map release: Mar 8, 2017 / Last update: Mar 8, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5x0m
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
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3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_6698.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.29 Å/pix.
= 258. Å
200 pix
1.29 Å/pix.
= 258. Å
200 pix
1.29 Å/pix.
= 258. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.29 Å
Contour Level:0.0465 (by author), 0.08 (movie #1):
Minimum - Maximum-0.26366407 - 0.391851
Average (Standard dev.)0.00046030077 (0.014029253)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 258 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.291.291.29
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z258.000258.000258.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.2640.3920.000

Supplemental data

Sample components

Entire voltage-gated sodium channel

EntireName: voltage-gated sodium channel / Number of components: 4

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

Cellular-componentName: voltage-gated sodium channel / Recombinant expression: No
SourceSpecies: Periplaneta americana / arthropod / ワモンゴキブリ
Source (engineered)Expression System: Homo sapiens / human

Component #2: protein, Sodium channel protein

ProteinName: Sodium channel protein / Recombinant expression: No
MassTheoretical: 183.875422 kDa
Source (engineered)Expression System: Periplaneta americana / arthropod / ワモンゴキブリ

Component #3: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINE / Number of Copies: 13 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

Component #4: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 25 mM Tris-HCl, pH 7.4, 50mM NaCl, 0.1% digitonin, 2.5 mM D-Desthiobiotin and protease inhibitor cocktail
pH: 7.4
VitrificationCryogen name: ETHANE / Temperature: 281 K / Humidity: 100 %
Details: Grids were blotted for 3.5 s and flash-frozen in liquid ethane cooled by liquid nitrogen.

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: 1.5625 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 22500 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 1373581
3D reconstructionSoftware: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

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