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- EMDB-3796: Subtomogram average of contracted contractile injection systems -

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Basic information

Entry
Database: EMDB / ID: EMD-3796
TitleSubtomogram average of contracted contractile injection systems
Map dataSubtomogram average of contracted contractile injection systems
Sample
  • Complex: Contracted contractile injection system
Biological speciesCandidatus Amoebophilus asiaticus 5a2 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 60.0 Å
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.
History
DepositionJul 10, 2017-
Header (metadata) releaseAug 16, 2017-
Map releaseAug 23, 2017-
UpdateAug 30, 2017-
Current statusAug 30, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 128
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 128
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3796.png

Downloads & links

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Map

FileDownload / File: emd_3796.map.gz / Format: CCP4 / Size: 263.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of contracted contractile injection systems
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.8 Å/pix.
x 28 pix.
= 386.4 Å		13.8 Å/pix.
x 86 pix.
= 1186.8 Å		13.8 Å/pix.
x 28 pix.
= 386.4 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: 13.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 128. / Movie #1: 128
Minimum - Maximum117.737939999999995 - 141.174479999999988
Average (Standard dev.)129.402919999999995 (±2.3367553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions862828
Spacing288628
CellA: 386.4 Å / B: 1186.8 Å / C: 386.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z13.813.813.8
M x/y/z288628
origin x/y/z0.0000.0000.000
length x/y/z386.4001186.800386.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288628
D min/max/mean117.738141.174129.403

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Supplemental data

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Additional map: Chimera-ready subtomogram average of contracted contractile injection systems...

Fileemd_3796_additional.map
AnnotationChimera-ready subtomogram average of contracted contractile injection systems
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Contracted contractile injection system

EntireName: Contracted contractile injection system
Components
  • Complex: Contracted contractile injection system

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Supramolecule #1: Contracted contractile injection system

SupramoleculeName: Contracted contractile injection system / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Candidatus Amoebophilus asiaticus 5a2 (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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 60.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 163
ExtractionNumber tomograms: 37 / Number images used: 163
Final angle assignmentType: OTHER

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