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- EMDB-16053: Subtomogram average of septal junctions from sepN-sfgfp mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-16053
TitleSubtomogram average of septal junctions from sepN-sfgfp mutant
Map data
Sample
  • Complex: Subtomogram average of septal junctions from sepN-sfgfp mutant
KeywordsCell-cell communication / Septal junctions / Filamentous cyanobacteria / Nostoc PCC 7120 / STRUCTURAL PROTEIN
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 41.0 Å
AuthorsKieninger A / Tokarz P / Janovic A / Pilhofer M / Weiss G / Maldener I
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK1708 Germany
Boehringer Ingelheim Fonds (BIF) Germany
Other government
CitationJournal: Nat Commun / Year: 2022
Title: SepN is a septal junction component required for gated cell-cell communication in the filamentous cyanobacterium Nostoc.
Authors: Ann-Katrin Kieninger / Piotr Tokarz / Ana Janović / Martin Pilhofer / Gregor L Weiss / Iris Maldener /
Abstract: Multicellular organisms require controlled intercellular communication for their survival. Strains of the filamentous cyanobacterium Nostoc regulate cell-cell communication between sister cells via a ...Multicellular organisms require controlled intercellular communication for their survival. Strains of the filamentous cyanobacterium Nostoc regulate cell-cell communication between sister cells via a conformational change in septal junctions. These multi-protein cell junctions consist of a septum spanning tube with a membrane-embedded plug at both ends, and a cap covering the plug on the cytoplasmic side. The identities of septal junction components are unknown, with exception of the protein FraD. Here, we identify and characterize a FraD-interacting protein, SepN, as the second component of septal junctions in Nostoc. We use cryo-electron tomography of cryo-focused ion beam-thinned cyanobacterial filaments to show that septal junctions in a sepN mutant lack a plug module and display an aberrant cap. The sepN mutant exhibits highly reduced cell-cell communication rates, as shown by fluorescence recovery after photobleaching experiments. Furthermore, the mutant is unable to gate molecule exchange through septal junctions and displays reduced filament survival after stress. Our data demonstrate the importance of controlling molecular diffusion between cells to ensure the survival of a multicellular organism.
History
DepositionOct 31, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16053.png

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Map

FileDownload / File: emd_16053.map.gz / Format: CCP4 / Size: 333 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
13.52 Å/pix.
x 44 pix.
= 594.88 Å		13.52 Å/pix.
x 44 pix.
= 594.88 Å		13.52 Å/pix.
x 44 pix.
= 594.88 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 13.52 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-3.3169231 - 3.378061
Average (Standard dev.)0.0028940183 (±0.69066525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions444444
Spacing444444
CellA=B=C: 594.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16053_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_16053_half_map_2.map
Projections & Slices
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Sample components

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Entire : Subtomogram average of septal junctions from sepN-sfgfp mutant

EntireName: Subtomogram average of septal junctions from sepN-sfgfp mutant
Components
  • Complex: Subtomogram average of septal junctions from sepN-sfgfp mutant

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Supramolecule #1: Subtomogram average of septal junctions from sepN-sfgfp mutant

SupramoleculeName: Subtomogram average of septal junctions from sepN-sfgfp mutant
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (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: 7.4 / Details: BG11 broth
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThin lamellae through plunge-frozen Nostoc filaments

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 41.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 118
ExtractionNumber tomograms: 22 / Number images used: 418
Final 3D classificationSoftware - Name: Dynamo
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: Dynamo

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