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- EMDB-55731: Subtomogram average of septal junctions from Nostoc PCC7120 wild type -

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Basic information

Entry
Database: EMDB / ID: EMD-55731
TitleSubtomogram average of septal junctions from Nostoc PCC7120 wild type
Map data
Sample
  • Complex: Septal junction from Nostoc PCC7120 wild type
Keywordsseptal junctions / Anabaena / Nostoc / cell-cell communication / TRANSPORT PROTEIN
Biological speciesNostoc PCC 7120 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 22.0 Å
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: To Be Published
Title: The FraD-SepN structural module serves as an anchor and assembly platform for septal junctions in cyanobacteria
Authors: Kieninger AK / Li Y / Janovic A / Tokarz P / Maldener I / Weiss GL
History
DepositionNov 17, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55731.png

Downloads & links

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Map

FileDownload / File: emd_55731.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.36 Å/pix.
x 72 pix.
= 385.56 Å		5.36 Å/pix.
x 72 pix.
= 385.56 Å		5.36 Å/pix.
x 72 pix.
= 385.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.355 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-6.5146894 - 6.804306
Average (Standard dev.)0.04511724 (±1.0364484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 385.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_55731_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55731_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Septal junction from Nostoc PCC7120 wild type

EntireName: Septal junction from Nostoc PCC7120 wild type
Components
  • Complex: Septal junction from Nostoc PCC7120 wild type

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Supramolecule #1: Septal junction from Nostoc PCC7120 wild type

SupramoleculeName: Septal junction from Nostoc PCC7120 wild type / 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
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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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 reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 9080
ExtractionNumber tomograms: 162 / Number images used: 10651 / Software - Name: Dynamo
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: NOT APPLICABLE

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