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- EMDB-4953: Electron cryotomogram of septal region from FIB milled Anabaena s... -

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Entry
Database: EMDB / ID: EMD-4953
TitleElectron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraD mutant filament
Map dataElectron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraD mutant filament
Sample
  • Cell: Electron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraD mutant filament
Biological speciesNostoc sp. PCC 7120 (bacteria)
Methodelectron tomography / cryo EM
AuthorsWeiss GL / Kieninger A / Maldener I / Forchhammer K / Pilhofer M
Funding support Germany, Switzerland, 3 items
OrganizationGrant numberCountry
German Research FoundationSFB766 Germany
European Research Council#679209 Switzerland
Swiss National Science Foundation#31003A_179255 Switzerland
CitationJournal: Cell / Year: 2019
Title: Structure and Function of a Bacterial Gap Junction Analog.
Authors: Gregor L Weiss / Ann-Katrin Kieninger / Iris Maldener / Karl Forchhammer / Martin Pilhofer /
Abstract: Multicellular lifestyle requires cell-cell connections. In multicellular cyanobacteria, septal junctions enable molecular exchange between sister cells and are required for cellular differentiation. ...Multicellular lifestyle requires cell-cell connections. In multicellular cyanobacteria, septal junctions enable molecular exchange between sister cells and are required for cellular differentiation. The structure of septal junctions is poorly understood, and it is unknown whether they are capable of controlling intercellular communication. Here, we resolved the in situ architecture of septal junctions by electron cryotomography of cryo-focused ion beam-milled cyanobacterial filaments. Septal junctions consisted of a tube traversing the septal peptidoglycan. Each tube end comprised a FraD-containing plug, which was covered by a cytoplasmic cap. Fluorescence recovery after photobleaching showed that intercellular communication was blocked upon stress. Gating was accompanied by a reversible conformational change of the septal junction cap. We provide the mechanistic framework for a cell junction that predates eukaryotic gap junctions by a billion years. The conservation of a gated dynamic mechanism across different domains of life emphasizes the importance of controlling molecular exchange in multicellular organisms.
History
DepositionMay 9, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseJul 24, 2019-
UpdateJul 24, 2019-
Current statusJul 24, 2019Processing 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_4953.png

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Map

FileDownload / File: emd_4953.map.gz / Format: CCP4 / Size: 288.9 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationElectron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraD mutant filament
Voxel sizeX=Y=Z: 13.51 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-6.744985 (±24.212633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1616170
Dimensions928960340
Spacing960928340
CellA: 12969.601 Å / B: 12537.28 Å / C: 4593.4 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/z960928340
origin x/y/z0.0000.0000.000
length x/y/z12969.60112537.2804593.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS16-16170
NC/NR/NS960928340
D min/max/mean-128.000127.000-6.745

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Supplemental data

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Sample components

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Entire : Electron cryotomogram of septal region from FIB milled Anabaena s...

EntireName: Electron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraD mutant filament
Components
  • Cell: Electron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraD mutant filament

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Supramolecule #1: Electron cryotomogram of septal region from FIB milled Anabaena s...

SupramoleculeName: Electron cryotomogram of septal region from FIB milled Anabaena sp. PCC7120 FraD mutant filament
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Nostoc sp. PCC 7120 (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 kV / Focused ion beam - Current: 18 nA / Focused ion beam - Duration: 1 sec. / Focused ion beam - Temperature: 128 K / Focused ion beam - Initial thickness: 3000 nm / Focused ion beam - Final thickness: 200 nm
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Helios NanoLab 600i. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is ...Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Helios NanoLab 600i. This is not in a list of allowed values set(['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: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 61

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