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- EMDB-50557: subtomogram averaging of the trans-envelope complex of a type 6 s... -

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Basic information

Entry
Database: EMDB / ID: EMD-50557
Titlesubtomogram averaging of the trans-envelope complex of a type 6 secretion system of Aureispira sp. CCB-QB1
Map data
Sample
  • Complex: Extracellular antenna of type 6 secretion system in Aureispira sp. CCB-QB1
Keywordstype 6 secretion system / bacterial predation / CONTRACTILE PROTEIN
Biological speciesAureispira sp. CCB-QB1 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
AuthorsLien Y-W / Amendola D / Lee KS / Bartlau N / Xu J / Furusawa G / Polz MF / Stocker R / Weiss GL / Pilhofer M
Funding support Switzerland, European Union, United States, 6 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_212592 Switzerland
European Research Council (ERC)679209European Union
European Research Council (ERC)101000232European Union
Simons Foundation542395 United States
Swiss National Science Foundation315230_176189 Switzerland
Simons Foundation572792 United States
CitationJournal: Science / Year: 2024
Title: Mechanism of bacterial predation via ixotrophy.
Authors: Yun-Wei Lien / Davide Amendola / Kang Soo Lee / Nina Bartlau / Jingwei Xu / Go Furusawa / Martin F Polz / Roman Stocker / Gregor L Weiss / Martin Pilhofer /
Abstract: Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be ...Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages we call "grappling hooks." Cryo-electron microscopy identified the grappling hooks as heptamers of a type IX secretion system substrate. After close predator-prey contact is established, cryo-electron tomography and functional assays showed that puncturing by a type VI secretion system mediated killing. Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker. Depending on nutrient availability, insertion sequence elements toggle the activity of ixotrophy. A marine metagenomic time series shows coupled dynamics of ixotrophic bacteria and prey. We found that the mechanism of ixotrophy involves multiple cellular machineries, is conserved, and may shape microbial populations in the environment.
History
DepositionJun 6, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50557.png

Downloads & links

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Map

FileDownload / File: emd_50557.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.91 Å/pix.
x 176 pix.
= 1216.16 Å		6.91 Å/pix.
x 176 pix.
= 1216.16 Å		6.91 Å/pix.
x 176 pix.
= 1216.16 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.4034996 - 2.784137
Average (Standard dev.)-0.11571569 (±0.19045213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions176176176
Spacing176176176
CellA=B=C: 1216.1599 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50557_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50557_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 : Extracellular antenna of type 6 secretion system in Aureispira sp...

EntireName: Extracellular antenna of type 6 secretion system in Aureispira sp. CCB-QB1
Components
  • Complex: Extracellular antenna of type 6 secretion system in Aureispira sp. CCB-QB1

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Supramolecule #1: Extracellular antenna of type 6 secretion system in Aureispira sp...

SupramoleculeName: Extracellular antenna of type 6 secretion system in Aureispira sp. CCB-QB1
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Aureispira sp. CCB-QB1 (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: 7.6
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: 2.62 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: 5.0 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: 30.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 334
ExtractionNumber tomograms: 146 / Number images used: 152
Final angle assignmentType: NOT APPLICABLE

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