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- EMDB-52694: Cryo-electron tomogram of the tip of Candidatus Arthromitus sp. S... -

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Basic information

Entry
Database: EMDB / ID: EMD-52694
TitleCryo-electron tomogram of the tip of Candidatus Arthromitus sp. SFB-rat-Yit (intracellular offspring containing intracellular plate-like structures) grown in rats
Map data
Sample
  • Cell: Candidatus Arthromitus sp. SFB-rat-Yit
KeywordsSegmented filamentous bacteria / UNKNOWN FUNCTION
Biological speciesCandidatus Arthromitus sp. SFB-rat-Yit (bacteria)
Methodelectron tomography / cryo EM
AuthorsCruz AR / Teo TH / Pehau-Arnaudet G / Winter JM / Gazi A / Sartori-Rupp A / Schnupf P
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)866222European Union
CitationJournal: To Be Published
Title: Segmented filamentous bacteria undergo a structural transition at their adhesive tip during unicellular to filament development.
Authors: Cruz AR / Wimmer B / Teo TH / Pehau-Arnaudet G / Winter JM / Gazi A / Lafaye P / Brier S / Legrand A / Dubrovsky-Gaupp A / Berard M / Ayme G / Sartori-Rupp A / Medalia O / Schnupf P
History
DepositionFeb 3, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52694.png

Downloads & links

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Map

FileDownload / File: emd_52694.map.gz / Format: CCP4 / Size: 3.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.02 Å/pix.
x 875 pix.
= 7019.25 Å		8.02 Å/pix.
x 1024 pix.
= 8214.528 Å		8.02 Å/pix.
x 1024 pix.
= 8214.528 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: 8.022 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-1217.487499999999955 - 449.748960000000011
Average (Standard dev.)14.428515000000001 (±18.763786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024875
Spacing10241024875
CellA: 8214.528 Å / B: 8214.528 Å / C: 7019.2505 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Candidatus Arthromitus sp. SFB-rat-Yit

EntireName: Candidatus Arthromitus sp. SFB-rat-Yit (bacteria)
Components
  • Cell: Candidatus Arthromitus sp. SFB-rat-Yit

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Supramolecule #1: Candidatus Arthromitus sp. SFB-rat-Yit

SupramoleculeName: Candidatus Arthromitus sp. SFB-rat-Yit / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Candidatus Arthromitus sp. SFB-rat-Yit (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 / Details: PBS
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: AURION / Diameter: 5 nm

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 0.95 sec. / Average electron dose: 4.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.11.X)
Details: SIRT-like filter also applied for the final reconstruction. Topaz denoise applied on the reconstructed tomogram using the default 10A/pixel model.
Number images used: 33
CTF correctionType: NONE

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