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- EMDB-55391: In situ cryo-electron tomogram of a mouse rod photoreceptor cell ... -

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Basic information

Entry
Database: EMDB / ID: EMD-55391
TitleIn situ cryo-electron tomogram of a mouse rod photoreceptor cell containing the centriolar luminal distal ring
Map data
Sample
  • Tissue: Mouse retina
Keywordscilia / flagella / photoreceptor / retina / transition zone / centriole / rod cell / rod photoreceptor / basal body / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsMukherjee S / Daraspe J / Genoud C / Hamel V / Guichard P
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3_187198 Switzerland
Swiss National Science Foundation310030_205087 Switzerland
Swiss State Secretariat for Education, Research and InnovationMB22.00075 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 16, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55391.png

Downloads & links

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Map

FileDownload / File: emd_55391.map.gz / Format: CCP4 / Size: 832 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.68 Å/pix.
x 416 pix.
= 4026.88 Å		9.68 Å/pix.
x 1024 pix.
= 9912.32 Å		9.68 Å/pix.
x 1024 pix.
= 9912.32 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: 9.68 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-32768.0 - 32767.0
Average (Standard dev.)4741.114999999999782 (±4148.029000000000451)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024416
Spacing10241024416
CellA: 9912.32 Å / B: 9912.32 Å / C: 4026.8801 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mouse retina

EntireName: Mouse retina
Components
  • Tissue: Mouse retina

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Supramolecule #1: Mouse retina

SupramoleculeName: Mouse retina / type: tissue / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57BL/6 J wild type / Organ: Eye / Tissue: Retina

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statetissue

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Sample preparation

BufferpH: 7
VitrificationCryogen name: NITROGEN
DetailsMouse retina
High pressure freezingInstrument: OTHER
Details: The value given for _em_high_pressure_freezing.instrument is Leica EM Ice. This is not in a list of allowed values {'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT', 'LEICA EM PACT2', ...Details: The value given for _em_high_pressure_freezing.instrument is Leica EM Ice. This is not in a list of allowed values {'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT', 'LEICA EM PACT2', 'OTHER', 'BAL-TEC HPM 010', 'LEICA EM HPM100'} so OTHER is written into the XML file.
Cryo protectant20% dextran
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: 2700 / Focused ion beam - Temperature: 81 K / Focused ion beam - Initial thickness: 4000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: Serialized Lift-Out procedure.. The value given for _em_focused_ion_beam.instrument is Thermo Scientific Aquilos 2 cryo-FIB-SEM. This is not in a list of allowed values ...Focused ion beam - Details: Serialized Lift-Out procedure.. The value given for _em_focused_ion_beam.instrument is Thermo Scientific Aquilos 2 cryo-FIB-SEM. 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: FEI FALCON IV (4k x 4k) / Average electron dose: 3.0 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: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD / Number images used: 61
CTF correctionSoftware - Name: IMOD / Type: PHASE FLIPPING ONLY

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