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- EMDB-2045: Subtomogram average of type VI secretion system (T6SS) sheath -

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Basic information

Entry
Database: EMDB / ID: EMD-2045
TitleSubtomogram average of type VI secretion system (T6SS) sheath
Map dataelectron cryotomography, sub-tomogram average
Sample
  • Sample: Type VI Secretion System sheath
  • Organelle or cellular component: Type VI Secretion Sheath
Keywordstype VI secretion system / T6SS / bacterial secretion / sheath / VipA / VipB / VipAB
Biological speciesVibrio cholerae (bacteria)
Methodsubtomogram averaging / cryo EM
AuthorsBasler M / Pilhofer M / Henderson GP / Jensen GJ / Mekalanos JJ
CitationJournal: Nature / Year: 2012
Title: Type VI secretion requires a dynamic contractile phage tail-like structure.
Authors: M Basler / M Pilhofer / G P Henderson / G J Jensen / J J Mekalanos /
Abstract: Type VI secretion systems are bacterial virulence-associated nanomachines composed of proteins that are evolutionarily related to components of bacteriophage tails. Here we show that protein ...Type VI secretion systems are bacterial virulence-associated nanomachines composed of proteins that are evolutionarily related to components of bacteriophage tails. Here we show that protein secretion by the type VI secretion system of Vibrio cholerae requires the action of a dynamic intracellular tubular structure that is structurally and functionally homologous to contractile phage tail sheath. Time-lapse fluorescence light microscopy reveals that sheaths of the type VI secretion system cycle between assembly, quick contraction, disassembly and re-assembly. Whole-cell electron cryotomography further shows that the sheaths appear as long tubular structures in either extended or contracted conformations that are connected to the inner membrane by a distinct basal structure. These data support a model in which the contraction of the type VI secretion system sheath provides the energy needed to translocate proteins out of effector cells and into adjacent target cells.
History
DepositionFeb 16, 2012-
Header (metadata) releaseFeb 23, 2012-
Map releaseMar 1, 2012-
UpdateFeb 27, 2013-
Current statusFeb 27, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: -120
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: -120
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EM-2045-T6SS...

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Map

FileDownload / File: emd_2045.map.gz / Format: CCP4 / Size: 1.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationelectron cryotomography, sub-tomogram average
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.3 Å/pix.
x 100 pix.
= 630. Å		6.3 Å/pix.
x 70 pix.
= 441. Å		6.3 Å/pix.
x 70 pix.
= 441. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 6.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: -100.0 / Movie #1: -120
Minimum - Maximum-209.621429440000014 - -48.78173065
Average (Standard dev.)-140.214828490000002 (±19.2406826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions7070100
Spacing7070100
CellA: 441.0 Å / B: 441.0 Å / C: 630.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.36.36.3
M x/y/z7070100
origin x/y/z0.0000.0000.000
length x/y/z441.000441.000630.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS7070100
D min/max/mean-209.621-48.782-140.215

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Supplemental data

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Sample components

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Entire : Type VI Secretion System sheath

EntireName: Type VI Secretion System sheath
Components
  • Sample: Type VI Secretion System sheath
  • Organelle or cellular component: Type VI Secretion Sheath

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Supramolecule #1000: Type VI Secretion System sheath

SupramoleculeName: Type VI Secretion System sheath / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Type VI Secretion Sheath

SupramoleculeName: Type VI Secretion Sheath / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Vibrio cholerae (bacteria) / Strain: 2740-80

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferpH: 7.4 / Details: 50mM Tris, 150mM NaCl
GridDetails: R 2/2 Quantifoil
VitrificationCryogen name: OTHER / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: GIF Gatan
DateMay 30, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 34000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsAverage number of tilts used in the 3D reconstructions: 120. Average tomographic tilt angle increment: 2.
Final reconstructionAlgorithm: OTHER / Software - Name: ETOMO,RAPTOR

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