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- EMDB-13770: Cryo-electron tomogram of cryo-FIB milled Anabaena PCC 7120 -

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Basic information

Entry
Database: EMDB / ID: EMD-13770
TitleCryo-electron tomogram of cryo-FIB milled Anabaena PCC 7120
Map dataCryo-electron tomogram of cryo-FIB milled Anabaena PCC7120 revealed thylakoid-anchored contractile injection systems
Sample
  • Cell: Septal region of a cryo-FIB milled Anabaena PCC 7120 filament
KeywordscryoET / cyanobacteria / contractile injection systems / CIS / CONTRACTILE PROTEIN
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodelectron tomography / cryo EM
AuthorsWeiss GL / Eisenstein F / Pilhofer M
Funding support Japan, 6 items
OrganizationGrant numberCountry
European Research Council (ERC)679209 Japan
Swiss National Science Foundation31003A_179255 Japan
Boehringer Ingelheim Fonds (BIF) Japan
German Research Foundation (DFG)SFB766 Japan
German Research Foundation (DFG)GRK1708 Japan
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Microbiol / Year: 2022
Title: Structure of a thylakoid-anchored contractile injection system in multicellular cyanobacteria.
Authors: Gregor L Weiss / Fabian Eisenstein / Ann-Katrin Kieninger / Jingwei Xu / Hannah A Minas / Milena Gerber / Miki Feldmüller / Iris Maldener / Karl Forchhammer / Martin Pilhofer /
Abstract: Contractile injection systems (CISs) mediate cell-cell interactions by phage tail-like structures, using two distinct modes of action: extracellular CISs are released into the medium, while type 6 ...Contractile injection systems (CISs) mediate cell-cell interactions by phage tail-like structures, using two distinct modes of action: extracellular CISs are released into the medium, while type 6 secretion systems (T6SSs) are attached to the cytoplasmic membrane and function upon cell-cell contact. Here, we characterized a CIS in the multicellular cyanobacterium Anabaena, with features distinct from extracellular CISs and T6SSs. Cryo-electron tomography of focused ion beam-milled cells revealed that CISs were anchored in thylakoid membrane stacks, facing the cell periphery. Single particle cryo-electron microscopy showed that this unique in situ localization was mediated by extensions of tail fibre and baseplate components. On stress, cyanobacteria induced the formation of ghost cells, presenting thylakoid-anchored CISs to the environment. Functional assays suggest that these CISs may mediate ghost cell formation and/or interactions of ghost cells with other organisms. Collectively, these data provide a framework for understanding the evolutionary re-engineering of CISs and potential roles of these CISs in cyanobacterial programmed cell death.
History
DepositionOct 21, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing 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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Supplemental images

emd_13770.png

Downloads & links

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Map

FileDownload / File: emd_13770.map.gz / Format: CCP4 / Size: 322.9 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationCryo-electron tomogram of cryo-FIB milled Anabaena PCC7120 revealed thylakoid-anchored contractile injection systems
Voxel sizeX=Y=Z: 13.51 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-3.4305289 (±24.041536000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin16-16-190
Dimensions928960380
Spacing960928380
CellA: 12969.601 Å / B: 12537.28 Å / C: 5133.8003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z13.51000104166713.5113.51
M x/y/z960928380
origin x/y/z0.0000.0000.000
length x/y/z12969.60112537.2805133.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS-1616-190
NC/NR/NS960928380
D min/max/mean-128.000127.000-3.431

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Supplemental data

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Sample components

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Entire : Septal region of a cryo-FIB milled Anabaena PCC 7120 filament

EntireName: Septal region of a cryo-FIB milled Anabaena PCC 7120 filament
Components
  • Cell: Septal region of a cryo-FIB milled Anabaena PCC 7120 filament

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Supramolecule #1: Septal region of a cryo-FIB milled Anabaena PCC 7120 filament

SupramoleculeName: Septal region of a cryo-FIB milled Anabaena PCC 7120 filament
type: cell / ID: 1 / Parent: 0
Details: Several thylakoid membrane-anchored contractile injection systems are visible
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (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: 7.4
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.024 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 128 K / Focused ion beam - Initial thickness: 3000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is TFS Helios NanoLab 600i. 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 QUANTUM (4k x 4k) / Average electron dose: 2.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 61

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