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- EMDB-55734: Cryo-electron tomogram of septal region from Nostoc PCC7120 FraD-TM -

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Basic information

Entry
Database: EMDB / ID: EMD-55734
TitleCryo-electron tomogram of septal region from Nostoc PCC7120 FraD-TM
Map data
Sample
  • Complex: Cryo-electron tomogram of septal region from Nostoc PCC7120 FraD-TM
Keywordsseptal junctions / Anabaena / Nostoc / cell-cell communication / TRANSPORT PROTEIN
Biological speciesNostoc PCC 7120 (bacteria)
Methodelectron tomography / cryo EM
AuthorsKieninger AK / Li Y / Janovic A / Tokarz P / Maldener I / Weiss GL
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationTMSGI3_226208 Switzerland
CitationJournal: Cell Rep / Year: 2026
Title: The SepN-FraD structural module serves as an anchor and assembly platform for septal junctions in cyanobacteria.
Authors: Ann-Katrin Kieninger / Yanxun Li / Ana Janović / Evert Haanappel / Piotr Tokarz / Marc Gueroult / Matthieu Chavent / Iris Maldener / Gregor L Weiss /
Abstract: Intercellular communication is essential for multicellularity. In filamentous cyanobacteria such as Nostoc sp. PCC 7120, communication occurs through septal junctions (SJs) that traverse the septum ...Intercellular communication is essential for multicellularity. In filamentous cyanobacteria such as Nostoc sp. PCC 7120, communication occurs through septal junctions (SJs) that traverse the septum and connect neighboring cells. Although the SJ components FraD and SepN are essential for SJ formation, their precise roles and spatial organization remain unclear. Here, we combine cryo-electron tomography, AlphaFold 3 structure prediction, and molecular dynamics simulation to refine the SJ architecture. We identify previously unresolved structural features, including a continuous, membrane-like tube connecting septal junction heads of neighboring cells and membrane-anchoring modules linking the plug to the periplasmic space. Structural modeling positions SepN as the plug-forming component and FraD as a membrane-spanning anchor with a periplasmic domain. Functional analyses demonstrate that the FraD periplasmic domain is required for proper nanopore formation, SJ assembly, and diazotrophic growth. Together, these findings establish the SepN-FraD module as the structural scaffold essential for SJ integrity and gating.
History
DepositionNov 17, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55734.png

Downloads & links

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Map

FileDownload / File: emd_55734.map.gz / Format: CCP4 / Size: 680.6 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.71 Å/pix.
x 242 pix.
= 2591.82 Å		10.71 Å/pix.
x 1440 pix.
= 15422.4 Å		10.71 Å/pix.
x 1024 pix.
= 10967.04 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: 10.71 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-5912.0 - 3894.0
Average (Standard dev.)42.845849999999999 (±355.968869999999981)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-209208-121
Dimensions14401024242
Spacing10241440242
CellA: 10967.04 Å / B: 15422.4 Å / C: 2591.82 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 septal region from Nostoc PCC7120 FraD-TM

EntireName: Cryo-electron tomogram of septal region from Nostoc PCC7120 FraD-TM
Components
  • Complex: Cryo-electron tomogram of septal region from Nostoc PCC7120 FraD-TM

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Supramolecule #1: Cryo-electron tomogram of septal region from Nostoc PCC7120 FraD-TM

SupramoleculeName: Cryo-electron tomogram of septal region from Nostoc PCC7120 FraD-TM
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Nostoc PCC 7120 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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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: 0.05 / Focused ion beam - Duration: 1200 / Focused ion beam - Temperature: 122 K / Focused ion beam - Initial thickness: 3000 / Focused ion beam - Final thickness: 180
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Zeiss Crossbeam. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 3.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 41
CTF correctionType: PHASE FLIPPING ONLY

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