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- EMDB-51206: Sub-tomogram average of contracted sheath complex in H. borinquen... -

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Basic information

Entry
Database: EMDB / ID: EMD-51206
TitleSub-tomogram average of contracted sheath complex in H. borinquense with C6 symmetry.
Map data
Sample
  • Cell: Halogeometricum borinquense
KeywordscryoET / type VI secretion system / archaea / antagonism. / STRUCTURAL PROTEIN
Biological speciesHalogeometricum borinquense DSM 11551 (archaea)
Methodsubtomogram averaging / cryo EM / Resolution: 60.0 Å
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_51206.png

Downloads & links

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Map

FileDownload / File: emd_51206.map.gz / Format: CCP4 / Size: 251 KB / 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 40 pix.
= 544. Å		13.6 Å/pix.
x 40 pix.
= 544. Å		13.6 Å/pix.
x 40 pix.
= 544. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 13.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-4.320519 - 2.3997054
Average (Standard dev.)0.05107128 (±0.8208144)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions404040
Spacing404040
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51206_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51206_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE-PROPANE

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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 reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 60.0 Å / Resolution method: OTHER
Details: The resolution was not determined due to the poor contrast of tomograms, which resulted from high intracellular salt concentration.
Number subtomograms used: 1138
ExtractionNumber tomograms: 34 / Number images used: 34
Final angle assignmentType: ANGULAR RECONSTITUTION

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