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- EMDB-55386: Tomogram of a mouse tracheal epithelial cell containing the C2CD3... -

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Basic information

Entry
Database: EMDB / ID: EMD-55386
TitleTomogram of a mouse tracheal epithelial cell containing the C2CD3 luminal ring protein
Map dataRaw tomogram reconstructed by filtered backprojection with IMOD.
Sample
  • Cell: Mouse epithelial tracheal cell
Keywordscilia / flagella / epithelium / transition zone / centriole / TRANSPORT PROTEIN / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
Authorsvan den Hoek HG / McCafferty C / Righetto RD / Stearns T / Engel BD
Funding support United States, Switzerland, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130286 United States
Swiss National Science Foundation Switzerland
CitationJournal: PLoS Biol / Year: 2025
Title: The luminal ring protein C2CD3 acts as a radial in-to-out organizer of the distal centriole and appendages.
Authors: Eloïse Bertiaux / Vincent Louvel / Caitlyn L McCafferty / Hugo van den Hoek / Umut Batman / Souradip Mukherjee / Lorène Bournonville / Olivier Mercey / Isabelle Méan / Ricardo D Righetto ...Authors: Eloïse Bertiaux / Vincent Louvel / Caitlyn L McCafferty / Hugo van den Hoek / Umut Batman / Souradip Mukherjee / Lorène Bournonville / Olivier Mercey / Isabelle Méan / Ricardo D Righetto / Adrian Müller / Philippe Van der Stappen / Garrison Buss / Jean Daraspe / Christel Genoud / Tim Stearns / Benjamin D Engel / Virginie Hamel / Paul Guichard /
Abstract: Centrioles are polarized microtubule-based structures with appendages at their distal end that are essential for cilia formation and function. The protein C2CD3 is critical for distal appendage ...Centrioles are polarized microtubule-based structures with appendages at their distal end that are essential for cilia formation and function. The protein C2CD3 is critical for distal appendage assembly, with mutations linked to orofaciodigital syndrome and other ciliopathies. However, its precise molecular role in appendage recruitment remains unclear. Using ultrastructure expansion microscopy (U-ExM) and iterative U-ExM on human cells, together with in situ cryo-electron tomography (cryo-ET) on mouse tissues, we reveal that C2CD3 adopts a radially symmetric 9-fold organization within the centriole's distal lumen. We show that the C-terminal region of C2CD3 localizes close to a ~100 nm luminal ring structure consisting of ~27 nodes, while its N-terminal region localizes close to a hook-like structure that attaches to the A-microtubule as it extends from the centriole interior to exterior. This hook structure is adjacent to the DISCO complex (MNR/CEP90/OFD1), which marks future appendage sites. C2CD3 depletion disrupts not only the recruitment of the DISCO complex via direct interaction with MNR but also destabilizes the luminal ring network composed of C2CD3/SFI1/centrin-2/CEP135/NA14, as well as the distal microtubule tip protein CEP162. This reveals an intricate "in-to-out" molecular hub connecting the centriolar lumen, distal microtubule cap, and appendages. Although C2CD3 loss results in shorter centrioles and appendage defects, key structural elements remain intact, permitting continued centriole duplication. We propose that C2CD3 forms the luminal ring structure and extends radially to the space between triplet microtubules, functioning as an architectural hub that scaffolds the distal end of the centriole, orchestrating its assembly and directing appendage formation.
History
DepositionOct 15, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55386.png

Downloads & links

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Map

FileDownload / File: emd_55386.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRaw tomogram reconstructed by filtered backprojection with IMOD.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.08 Å/pix.
x 464 pix.
= 6533.12 Å		14.08 Å/pix.
x 928 pix.
= 13066.24 Å		14.08 Å/pix.
x 928 pix.
= 13066.24 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: 14.08 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-2091.416499999999814 - 1486.397200000000112
Average (Standard dev.)54.704666000000003 (±151.60408000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-232
Dimensions928928464
Spacing928928464
CellA: 13066.24 Å / B: 13066.24 Å / C: 6533.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Tomogram denoised by cryo-CARE.

Fileemd_55386_additional_1.map
AnnotationTomogram denoised by cryo-CARE.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Tomogram denoised by IsoNet on top of cryo-CARE.

Fileemd_55386_additional_2.map
AnnotationTomogram denoised by IsoNet on top of cryo-CARE.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mouse epithelial tracheal cell

EntireName: Mouse epithelial tracheal cell
Components
  • Cell: Mouse epithelial tracheal cell

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Supramolecule #1: Mouse epithelial tracheal cell

SupramoleculeName: Mouse epithelial tracheal cell / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse) / Strain: wild-type CD-1 or GFPcentrin2 transgenic mice / Organ: Trachea / Tissue: Epithelium

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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
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Instrument: LEICA EM GP
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 2700 / Focused ion beam - Temperature: 91 K / Focused ion beam - Initial thickness: 13000 / Focused ion beam - Final thickness: 130
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Aquilos. 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 K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 59
CTF correctionSoftware - Name: IMOD / Type: PHASE FLIPPING ONLY

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