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- EMDB-52774: Cryo-electron tomogram of cryo-FIB milled Nostoc PCC7120 wild-type -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52774
TitleCryo-electron tomogram of cryo-FIB milled Nostoc PCC7120 wild-type
Map data
Sample
  • Cell: Septum of Nostoc PCC7120 wild-type
KeywordsSeptal junctions / STRUCTURAL PROTEIN
Biological speciesNostoc PCC7120 (bacteria)
Methodelectron tomography / cryo EM
AuthorsMueller T / Kleusberg FM / Roganowicz K / Weiss G / Coles M / Selim KA
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
ETH Zurich Switzerland
CitationJournal: To Be Published
Title: The Ca2+-binding protein CSE links Ca2+-signaling with gated cell-cell communication in multicellular cyanobacteria
Authors: Mueller T / Kleusberg FM / Roganowicz K / Weiss G / Coles M / Selim KA
History
DepositionFeb 7, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52774.png

Downloads & links

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Map

FileDownload / File: emd_52774.map.gz / Format: CCP4 / Size: 2.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.74 Å/pix.
x 400 pix.
= 4296. Å		10.74 Å/pix.
x 1440 pix.
= 15465.6 Å		10.74 Å/pix.
x 1022 pix.
= 10976.279 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: 10.74 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-7.9782443 - 2.6922393
Average (Standard dev.)-0.47128555 (±0.28696322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions14401022400
Spacing10221440400
CellA: 10976.279 Å / B: 15465.6 Å / C: 4296.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Septum of Nostoc PCC7120 wild-type

EntireName: Septum of Nostoc PCC7120 wild-type
Components
  • Cell: Septum of Nostoc PCC7120 wild-type

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Supramolecule #1: Septum of Nostoc PCC7120 wild-type

SupramoleculeName: Septum of Nostoc PCC7120 wild-type / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Nostoc PCC7120 (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: 7.5
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: 360 / Focused ion beam - Temperature: 123 K / Focused ion beam - Initial thickness: 1000 / 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: 5.7 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: 6.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 41
CTF correctionType: NONE

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