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- EMDB-50551: Cryo-electron tomogram of cryoFIB-milled Aureispira sp. CCB-QB1 a... -

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Basic information

Entry
Database: EMDB / ID: EMD-50551
TitleCryo-electron tomogram of cryoFIB-milled Aureispira sp. CCB-QB1 and Vibrio campbellii
Map data
Sample
  • Cell: Cryo-electron tomogram of cryoFIB-milled Aureispira sp. CCB-QB1 and Vibrio campbellii mixture
KeywordsType 6 secretion system / type 9 secretion system / bacterial predation / CONTRACTILE PROTEIN
Biological speciesAureispira sp. CCB-QB1 (bacteria)
Methodelectron tomography / cryo EM
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
Citation
Journal: 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.
#1: Journal: Biorxiv / Year: 2024
Title: Mechanism of bacterial predation via ixotrophy
Authors: Lien YW / Amendola D / Lee KS / Bartlau N / Xu J / Furusawa G / Polz MF / Stocker R / Weiss GL / Pilhofer M
History
DepositionJun 5, 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_50551.png

Downloads & links

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Map

FileDownload / File: emd_50551.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.82 Å/pix.
x 400 pix.
= 5528. Å		13.82 Å/pix.
x 928 pix.
= 12824.96 Å		13.82 Å/pix.
x 960 pix.
= 13267.199 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: 13.82 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-337.615479999999991 - 253.124239999999986
Average (Standard dev.)-0.00000000086576 (±11.979730999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928960400
Spacing960928400
CellA: 13267.199 Å / B: 12824.96 Å / C: 5528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-electron tomogram of cryoFIB-milled Aureispira sp. CCB-QB1 a...

EntireName: Cryo-electron tomogram of cryoFIB-milled Aureispira sp. CCB-QB1 and Vibrio campbellii mixture
Components
  • Cell: Cryo-electron tomogram of cryoFIB-milled Aureispira sp. CCB-QB1 and Vibrio campbellii mixture

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Supramolecule #1: Cryo-electron tomogram of cryoFIB-milled Aureispira sp. CCB-QB1 a...

SupramoleculeName: Cryo-electron tomogram of cryoFIB-milled Aureispira sp. CCB-QB1 and Vibrio campbellii mixture
type: cell / 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
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 20 / Focused ion beam - Duration: 900 / Focused ion beam - Temperature: 123 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 150
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 {'DB235', 'OTHER'} so OTHER is written into the XML file.

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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: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 61

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