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- EMDB-3800: Cryotomogram of intracellular amoebophili 2 hours post infection -

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Basic information

Entry
Database: EMDB / ID: EMD-3800
TitleCryotomogram of intracellular amoebophili 2 hours post infection
Map data
Sample
  • Cell: Amoebophilus asiaticus
Biological speciesCandidatus Amoebophilus asiaticus 5a2 (bacteria)
Methodelectron tomography / cryo EM
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
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Simplified surface model
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3800.png

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Map

FileDownload / File: emd_3800.map.gz / Format: CCP4 / Size: 287.5 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 23.82 Å
Density
Minimum - Maximum-128. - 127.
Average (Standard dev.)-11.638324000000001 (±20.430927000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00175
Dimensions928928350
Spacing928928350
CellA: 22104.959 Å / B: 22104.959 Å / C: 8337.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z23.81999892241423.81999892241423.82
M x/y/z928928350
origin x/y/z0.0000.0000.000
length x/y/z22104.95922104.9598337.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS00175
NC/NR/NS928928350
D min/max/mean-128.000127.000-11.638

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Supplemental data

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Sample components

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Entire : Amoebophilus asiaticus

EntireName: Amoebophilus asiaticus
Components
  • Cell: Amoebophilus asiaticus

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Supramolecule #1: Amoebophilus asiaticus

SupramoleculeName: Amoebophilus asiaticus / type: cell / 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
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.025 nA / Focused ion beam - Dose rate: 1 / Focused ion beam - Duration: 900 sec. / Focused ion beam - Temperature: 118 K / Focused ion beam - Initial thickness: 10000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Helios 600i. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.97 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 61

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