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- EMDB-3795: Subtomogram average of extended contractile injection systems -

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Basic information

Entry
Database: EMDB / ID: 3795
TitleSubtomogram average of extended contractile injection systems
Map dataSubtomogram average of extended contractile injection systems
SampleExtended contractile injection system:
SourceCandidatus Amoebophilus asiaticus 5a2 (bacteria)
Methodsubtomogram averaging / cryo EM / 40 Å resolution
AuthorsBoeck D / Medeiros JM
CitationJournal: Science / Year: 2017
Title: In situ architecture, function, and evolution of a contractile injection system.
Authors: Désirée Böck / João M Medeiros / Han-Fei Tsao / Thomas Penz / Gregor L Weiss / Karin Aistleitner / Matthias Horn / Martin Pilhofer
Abstract: Contractile injection systems mediate bacterial cell-cell interactions by a bacteriophage tail-like structure. In contrast to extracellular systems, the type 6 secretion system (T6SS) is defined by ...Contractile injection systems mediate bacterial cell-cell interactions by a bacteriophage tail-like structure. In contrast to extracellular systems, the type 6 secretion system (T6SS) is defined by intracellular localization and attachment to the cytoplasmic membrane. Here we used cryo-focused ion beam milling, electron cryotomography, and functional assays to study a T6SS in The in situ architecture revealed three modules, including a contractile sheath-tube, a baseplate, and an anchor. All modules showed conformational changes upon firing. Lateral baseplate interactions coordinated T6SSs in hexagonal arrays. The system mediated interactions with host membranes and may participate in phagosome escape. Evolutionary sequence analyses predicted that T6SSs are more widespread than previously thought. Our insights form the basis for understanding T6SS key concepts and exploring T6SS diversity.
Copyright: 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
DateDeposition: Jul 10, 2017 / Header (metadata) release: Aug 16, 2017 / Map release: Aug 23, 2017 / Last update: Aug 30, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 127
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 127
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3795.map.gz (map file in CCP4 format, 961 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
40 pix
8.1 Å/pix.
= 324. Å
150 pix
8.1 Å/pix.
= 1215. Å
40 pix
8.1 Å/pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.1 Å
Density
Contour Level:127 (by author), 127 (movie #1):
Minimum - Maximum117.34849 - 142.58835
Average (Standard dev.)127.8269 (2.1830807)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions1504040
Origin000
Limit1493939
Spacing4015040
CellA: 324 Å / B: 1215 Å / C: 324 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.18.18.1
M x/y/z4015040
origin x/y/z0.0000.0000.000
length x/y/z324.0001215.000324.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS4015040
D min/max/mean117.348142.588127.827

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Supplemental data

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Sample components

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Entire Extended contractile injection system

EntireName: Extended contractile injection system / Number of components: 1

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Component #1: protein, Extended contractile injection system

ProteinName: Extended contractile injection system / Recombinant expression: No
SourceSpecies: Candidatus Amoebophilus asiaticus 5a2 (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE-PROPANE MIXTURE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.24 e/Å2 / Illumination mode: OTHER
LensImaging mode: OTHER
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 40 Å / Resolution method: FSC 0.5 CUT-OFF

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