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- EMDB-4696: Volta phase plate in situ tomogram of an enteroaggregative Escher... -

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Entry
Database: EMDB / ID: EMD-4696
TitleVolta phase plate in situ tomogram of an enteroaggregative Escherichia coli cell displaying a type six secretion system apparatus.
Map dataVolta phase plate in situ tomogram of an enteroaggregative Escherichia coli cell displaying a type six secretion system apparatus.
Sample
  • Cell: Enteroaggregative Escherichia coli cell displaying a type six secretion system apparatus.
Biological speciesEscherichia coli 042 (bacteria)
Methodelectron tomography / cryo EM
AuthorsSzwedziak P / Pilhofer M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_152878 Switzerland
CitationJournal: Nat Commun / Year: 2019
Title: Bidirectional contraction of a type six secretion system.
Authors: Piotr Szwedziak / Martin Pilhofer /
Abstract: Contractile injection systems (CISs) mediate cell-cell interactions by a phage tail-like apparatus. Their conserved mechanism relies on the anchoring of the proximal end of a sheath-tube module to a ...Contractile injection systems (CISs) mediate cell-cell interactions by a phage tail-like apparatus. Their conserved mechanism relies on the anchoring of the proximal end of a sheath-tube module to a membrane, followed by contraction of the sheath towards the attachment site and ejection of the inner tube. Here we reveal a major variation of the CIS mechanism in the type six secretion system (T6SS) of enteroaggregative Escherichia coli (EAEC). We show that both ends of the sheath-tube module are attached to opposite sides of the cell, enabling the structure to contract in two opposite directions. The protein TssA1 mediates the interaction of the distal end with the cell envelope, the termination of tail elongation, and non-canonical contraction towards the distal end. We provide a framework for the molecular processes at the T6SS distal end. Further research will address whether bidirectional contraction allows for bidirectional effector secretion. The unrecognized concept of non-canonical contractions could be relevant to biofilms of the human intestine.
History
DepositionMar 13, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseMar 27, 2019-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

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  • Imaged by UCSF Chimera
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  • Imaged by UCSF Chimera
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Supplemental images

emd_4696.png

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Map

FileDownload / File: emd_4696.map.gz / Format: CCP4 / Size: 722.2 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationVolta phase plate in situ tomogram of an enteroaggregative Escherichia coli cell displaying a type six secretion system apparatus.
Voxel sizeX=Y=Z: 21.67 Å
Density
Minimum - Maximum-6297 - 4141
Average (Standard dev.)81.9009 (±162.68346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin21216-16
Dimensions425960928
Spacing960425928
CellA: 20803.2 Å / B: 9209.75 Å / C: 20109.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z21.66999895833321.6721.67
M x/y/z960425928
origin x/y/z0.0000.0000.000
length x/y/z20803.1999209.75020109.760
α/β/γ90.00090.00090.000
start NX/NY/NZ212211153
NX/NY/NZ80102186
MAP C/R/S123
start NC/NR/NS16212-16
NC/NR/NS960425928
D min/max/mean-6297.0004141.00081.901

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Supplemental data

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Sample components

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Entire : Enteroaggregative Escherichia coli cell displaying a type six sec...

EntireName: Enteroaggregative Escherichia coli cell displaying a type six secretion system apparatus.
Components
  • Cell: Enteroaggregative Escherichia coli cell displaying a type six secretion system apparatus.

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Supramolecule #1: Enteroaggregative Escherichia coli cell displaying a type six sec...

SupramoleculeName: Enteroaggregative Escherichia coli cell displaying a type six secretion system apparatus.
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli 042 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Cytodiagnostics / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 121

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