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- EMDB-52697: Cryo-electron tomogram of the tip of Candidatus Arthromitus sp. S... -

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Basic information

Entry
Database: EMDB / ID: EMD-52697
TitleCryo-electron tomogram of the tip of Candidatus Arthromitus sp. SFB-mouse-NL (unidentified stage intracellular offspring) grown in mice
Map data
Sample
  • Cell: Candidatus Arthromitus sp. SFB-mouse-NL
KeywordsSegmented filamentous bacteria / UNKNOWN FUNCTION
Biological speciesCandidatus Arthromitus sp. SFB-mouse-NL (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: Nat Commun / Year: 2025
Title: Segmented filamentous bacteria undergo a structural transition at their adhesive tip during unicellular to filament development.
Authors: Ana Raquel Cruz / Benedikt H Wimmer / Teck Hui Teo / Gérard Pehau-Arnaudet / Jean-Marie Winter / Anastasia D Gazi / Pierre Lafaye / Sébastien Brier / Agnès Legrand / Anna Dubrovsky-Gaupp ...Authors: Ana Raquel Cruz / Benedikt H Wimmer / Teck Hui Teo / Gérard Pehau-Arnaudet / Jean-Marie Winter / Anastasia D Gazi / Pierre Lafaye / Sébastien Brier / Agnès Legrand / Anna Dubrovsky-Gaupp / Marion Bérard / Gabriel Aymé / Anna Sartori-Rupp / Ohad Medalia / Pamela Schnupf /
Abstract: Segmented filamentous bacteria (SFB) are intestinal commensals that promote immune system development and pathogen protection through intimate attachment to the ileal epithelium. Attachment occurs ...Segmented filamentous bacteria (SFB) are intestinal commensals that promote immune system development and pathogen protection through intimate attachment to the ileal epithelium. Attachment occurs via the tip of unicellular teardrop-shaped SFB, called intracellular offsprings (IOs), before outgrowth into filaments. To characterize this critical stage of the SFB life cycle, we imaged SFB using cryo-electron microscopy and tomography. IOs were surrounded by a repetitive surface (S)-layer that became replaced by disordered hair-like structures specifically at the IO tip. During outgrowth into filaments, the S-layer was exchanged for a morphologically distinct repetitive hair-like layer. The bacterial structures and morphological transition were conserved across SFB from mouse and rat origin, while growth of mouse-SFB under non-attachment conditions in a heterologous host affected the SFB tip length and relative proportion of the tip stages. Moreover, a major Th17 and B cell antigen, while being a ubiquitous cell wall-associated protein, was immunologically accessible only at the filament tip, underscoring the unique properties of the tip structure. This study identifies an IO-specific S-layer and reveals a conserved developmental transition of the SFB tip surface including the transient appearance of structures consistent in location and timing with being involved in host cell attachment.
History
DepositionFeb 3, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52697.png

Downloads & links

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Map

FileDownload / File: emd_52697.map.gz / Format: CCP4 / Size: 2.4 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 625 pix.
= 5013.75 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-1079.010099999999966 - 416.964999999999975
Average (Standard dev.)12.875038999999999 (±16.115189000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024625
Spacing10241024625
CellA: 8214.528 Å / B: 8214.528 Å / C: 5013.75 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-mouse-NL

EntireName: Candidatus Arthromitus sp. SFB-mouse-NL (bacteria)
Components
  • Cell: Candidatus Arthromitus sp. SFB-mouse-NL

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Supramolecule #1: Candidatus Arthromitus sp. SFB-mouse-NL

SupramoleculeName: Candidatus Arthromitus sp. SFB-mouse-NL / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Candidatus Arthromitus sp. SFB-mouse-NL (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: 6.0 µm / Nominal defocus min: 6.0 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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