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- EMDB-51203: Cryo-electron tomogram of H. borinquense showing extended T6SS complex -

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Basic information

Entry
Database: EMDB / ID: EMD-51203
TitleCryo-electron tomogram of H. borinquense showing extended T6SS complex
Map data
Sample
  • Cell: Halogeometricum borinquense
KeywordscryoET / type VI secretion system / archaea / antagonism. / STRUCTURAL PROTEIN
Biological speciesHalogeometricum borinquense DSM 11551 (archaea)
Methodelectron tomography / cryo EM
AuthorsZachs T / Malit JJ / Xu J / Schuerch A / Sivabalasarma S / Nussbaum P / Albers SV / Pilhofer M
Funding support Switzerland, European Union, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_212592 Switzerland
European Research Council (ERC)679209European Union
European Research Council (ERC)101000232European Union
CitationJournal: Sci Adv / Year: 2024
Title: Archaeal type six secretion system mediates contact-dependent antagonism.
Authors: Tobias Zachs / Jessie James L Malit / Jingwei Xu / Alexandra Schürch / Shamphavi Sivabalasarma / Phillip Nußbaum / Sonja-Verena Albers / Martin Pilhofer /
Abstract: Microbial communities are shaped by cell-cell interactions. Although archaea are often found in associations with other microorganisms, the mechanisms structuring these communities are poorly ...Microbial communities are shaped by cell-cell interactions. Although archaea are often found in associations with other microorganisms, the mechanisms structuring these communities are poorly understood. Here, we report on the structure and function of haloarchaeal contractile injection systems (CISs). Using a combination of functional assays and time-lapse imaging, we show that exhibits antagonism toward by inducing cell lysis and inhibiting proliferation. This antagonism is contact-dependent and requires a functional CIS, which is encoded by a gene cluster that is associated with toxin-immunity pairs. Cryo-focused ion beam milling and imaging by cryo-electron tomography revealed that these CISs are bound to the cytoplasmic membrane, resembling the bacterial type six secretion systems (T6SSs). We show that related T6SS gene clusters are conserved and expressed in other haloarchaeal strains, which exhibit antagonistic behavior. Our data provide a mechanistic framework for understanding how archaea may shape microbial communities and affect the food webs they inhabit.
History
DepositionJul 30, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51203.png

Downloads & links

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Map

FileDownload / File: emd_51203.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.6 Å/pix.
x 500 pix.
= 6800. Å		13.6 Å/pix.
x 1440 pix.
= 19584. Å		13.6 Å/pix.
x 1024 pix.
= 13926.4 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 13.6 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-659.311000000000035 - 604.374450000000024
Average (Standard dev.)-0.000000000248422 (±24.377022)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions14401024500
Spacing10241440500
CellA: 13926.4 Å / B: 19584.0 Å / C: 6800.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Halogeometricum borinquense

EntireName: Halogeometricum borinquense
Components
  • Cell: Halogeometricum borinquense

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Supramolecule #1: Halogeometricum borinquense

SupramoleculeName: Halogeometricum borinquense / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Halogeometricum borinquense DSM 11551 (archaea)

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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: 7.2
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 120 K / Focused ion beam - Initial thickness: 800 / Focused ion beam - Final thickness: 250
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Zeiss Crossbeam 550. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 130.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 41

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