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- EMDB-8600: Sub-tomogram average of the type VI secretion system membrane-ass... -

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Basic information

Entry
Database: EMDB / ID: EMD-8600
TitleSub-tomogram average of the type VI secretion system membrane-associated region in Myxococcus xanthusType VI secretion system
Map data
Sample
  • Complex: Type VI secretion system
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 40.0 Å
AuthorsChang Y-W / Rettberg LA / Jensen GJ
CitationJournal: EMBO Rep / Year: 2017
Title: structures of an intact type VI secretion system revealed by electron cryotomography.
Authors: Yi-Wei Chang / Lee A Rettberg / Davi R Ortega / Grant J Jensen /
Abstract: The type VI secretion system (T6SS) is a versatile molecular weapon used by many bacteria against eukaryotic hosts or prokaryotic competitors. It consists of a cytoplasmic bacteriophage tail-like ...The type VI secretion system (T6SS) is a versatile molecular weapon used by many bacteria against eukaryotic hosts or prokaryotic competitors. It consists of a cytoplasmic bacteriophage tail-like structure anchored in the bacterial cell envelope via a cytoplasmic baseplate and a periplasmic membrane complex. Rapid contraction of the sheath in the bacteriophage tail-like structure propels an inner tube/spike complex through the target cell envelope to deliver effectors. While structures of purified contracted sheath and purified membrane complex have been solved, because sheaths contract upon cell lysis and purification, no structure is available for the extended sheath. Structural information about the baseplate is also lacking. Here, we use electron cryotomography to directly visualize intact T6SS structures inside cells. Using sub-tomogram averaging, we resolve the structure of the extended sheath and membrane-associated components including the baseplate. Moreover, we identify novel extracellular bacteriophage tail fiber-like antennae. These results provide new structural insights into how the extended sheath prevents premature disassembly and how this sophisticated machine may recognize targets.
History
DepositionFeb 13, 2017-
Header (metadata) releaseFeb 22, 2017-
Map releaseMay 10, 2017-
UpdateJul 12, 2017-
Current statusJul 12, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.65
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.65
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8600.png

Downloads & links

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Map

FileDownload / File: emd_8600.map.gz / Format: CCP4 / Size: 7.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.8 Å/pix.
x 100 pix.
= 780. Å		7.8 Å/pix.
x 200 pix.
= 1560. Å		7.8 Å/pix.
x 100 pix.
= 780. 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: 7.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65 / Movie #1: 0.65
Minimum - Maximum-0.000000029802322 - 1.
Average (Standard dev.)0.43400806 (±0.105681956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200100100
Spacing100200100
CellA: 780.0 Å / B: 1560.0 Å / C: 780.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.87.87.8
M x/y/z100200100
origin x/y/z0.0000.0000.000
length x/y/z780.0001560.000780.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-41
NX/NY/NZ737384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100200100
D min/max/mean-0.0001.0000.434

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Supplemental data

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Sample components

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Entire : Type VI secretion system

EntireName: Type VI secretion system
Components
  • Complex: Type VI secretion system

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Supramolecule #1: Type VI secretion system

SupramoleculeName: Type VI secretion system / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Myxococcus xanthus DK 1622 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 16 / Number images used: 16 / Software - Name: PEET
CTF correctionSoftware - Name: IMOD
Final 3D classificationSoftware - Name: PEET
Final angle assignmentType: OTHER / Software - Name: PEET
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: OTHER / Software - Name: Tomo3d / Number subtomograms used: 16

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