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- EMDB-3564: Subtomogram average of type VI secretion system (T6SS) contracted... -

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Basic information

Database: EMDB / ID: 3564
TitleSubtomogram average of type VI secretion system (T6SS) contracted sheath
SampleType VI secretion system contracted sheath
SourceVibrio cholerae / bacteria / コレラ菌, ビブリオ・コレラエ
Map data
Methodsubtomogram averaging, at 17.4 Å resolution
AuthorsWang J / Basler M
CitationTo Be Published

To Be Published Search PubMed
Structure and mechanism of contraction of the extended Type VI secretion system sheath
Wang J / Basler M

DateDeposition: Jan 4, 2017 / Header (metadata) release: Feb 8, 2017 / Map release: Aug 2, 2017 / Last update: Aug 2, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 2.2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.2
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_3564.map.gz (map file in CCP4 format, 4371 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
104 pix
5.2 Å/pix.
= 540.8 Å
103 pix
5.2 Å/pix.
= 535.6 Å
102 pix
5.2 Å/pix.
= 530.4 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 5.2 Å
Contour Level:2.2 (by author), 2.2 (movie #1):
Minimum - Maximum-6.846825 - 4.58572
Average (Standard dev.)-0.69555193 (1.4460508)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 530.39996 Å / B: 535.6 Å / C: 540.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.25.25.2
M x/y/z102103104
origin x/y/z0.0000.0000.000
length x/y/z530.400535.600540.800
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-10-10-10
D min/max/mean-6.8474.586-0.696

Supplemental data

Sample components

Entire Type VI secretion system contracted sheath

EntireName: Type VI secretion system contracted sheath / Number of components: 3

Component #1: cellular-component, Type VI secretion system contracted sheath

Cellular-componentName: Type VI secretion system contracted sheath / Recombinant expression: No
SourceSpecies: Vibrio cholerae / bacteria / コレラ菌, ビブリオ・コレラエ

Component #2: protein, vipA

ProteinName: vipA / Recombinant expression: No

Component #3: protein, vipB

ProteinName: vipB / Recombinant expression: No

Experimental details

Sample preparation

Specimen statehelical array
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 17.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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