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- EMDB-54241: Cryo sub-tomogram average of A-C linker from FIB-milled Tetrahyme... -

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Basic information

Entry
Database: EMDB / ID: EMD-54241
TitleCryo sub-tomogram average of A-C linker from FIB-milled Tetrahymena cells
Map data
Sample
  • Cell: Tetrahymena thermophile
Keywordscentriole / basal body / centrosome / STRUCTURAL PROTEIN
Biological speciesTetrahymena thermophila (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
AuthorsCai B / Xu JW / Luo L / Aarts E / Leitner A / Ishikawa T / Beltro P / Pilhofer M / Wieczorek M
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
ETH ZurichETH-22 22-1 Switzerland
Swiss National Science Foundation320030-231677 Switzerland
Swiss National Science FoundationIZLIZ3 200294 Switzerland
CitationJournal: Sci Adv / Year: 2025
Title: Structure and assembly of the A-C linker connecting microtubule triplets in centrioles.
Authors: Bin Cai / Jingwei Xu / Erik H Collet / Ellen Aarts / Leo Luo / Alexander Leitner / Takashi Ishikawa / Pedro Beltrao / Chad G Pearson / Martin Pilhofer / Michal Wieczorek /
Abstract: Centriole assembly involves the coordination of centriolar modules. One module is the A-C linker, an enigmatic protein assembly connecting the A-microtubule of one microtubule triplet to the C- ...Centriole assembly involves the coordination of centriolar modules. One module is the A-C linker, an enigmatic protein assembly connecting the A-microtubule of one microtubule triplet to the C-microtubule of the neighboring triplet. Here, we integrated biochemistry, multiscale cryo-electron microscopy, and AlphaFold modeling to investigate the architecture of the centriole. Using an improved centriole isolation method, we determined the structure of the A-C linker bound to microtubule triplets, which revealed how the A-C linker cross-links microtubules and integrates with the B-C junction. We found marked changes in the structure and composition of the A-C linker that correlate with the presence of other centriolar modules, including the pinhead, cartwheel, and inner scaffold. Our findings show that the A-C linker is a highly integrated component of the centriole whose polymorphism may orchestrate the assembly of spatially distinct centriolar modules, and provide a framework for dissecting the biology of centrioles.
History
DepositionJul 2, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54241.png

Downloads & links

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Map

FileDownload / File: emd_54241.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.02 Å/pix.
x 96 pix.
= 865.92 Å		9.02 Å/pix.
x 96 pix.
= 865.92 Å		9.02 Å/pix.
x 96 pix.
= 865.92 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 9.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-4.0999155 - 4.2224736
Average (Standard dev.)0.13871245 (±0.6784677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 865.92004 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54241_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_54241_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_54241_half_map_2.map
Projections & Slices
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Sample components

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Entire : Tetrahymena thermophile

EntireName: Tetrahymena thermophile
Components
  • Cell: Tetrahymena thermophile

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Supramolecule #1: Tetrahymena thermophile

SupramoleculeName: Tetrahymena thermophile / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 3.17 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: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 1809
ExtractionNumber tomograms: 14 / Number images used: 1809 / Software - Name: Dynamo
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: ANGULAR RECONSTITUTION

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