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- EMDB-53987: Composite map of Tetrahymena transitional A-C linker -

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Basic information

Entry
Database: EMDB / ID: EMD-53987
TitleComposite map of Tetrahymena transitional A-C linker
Map dataComposite map of Tetrahymena transitional A-C linker
Sample
  • Organelle or cellular component: Transitional A-C linker of Tetrahymena basal body centriole
Keywordscentriole / basal body / centrosome / STRUCTURAL PROTEIN
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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
DepositionJun 10, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53987.png

Downloads & links

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Map

FileDownload / File: emd_53987.map.gz / Format: CCP4 / Size: 199.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of Tetrahymena transitional A-C linker
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 534 pix.
= 702.21 Å		1.32 Å/pix.
x 348 pix.
= 457.62 Å		1.32 Å/pix.
x 282 pix.
= 370.83 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.315 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.5
Minimum - Maximum0.0 - 16.366250000000001
Average (Standard dev.)0.24969855 (±1.0868908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-105-5-230
Dimensions348282534
Spacing282348534
CellA: 370.83002 Å / B: 457.62003 Å / C: 702.21 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Initial consensus refinement of transitional A-C linker

Fileemd_53987_additional_1.map
AnnotationInitial consensus refinement of transitional A-C linker
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Transitional A-C linker of Tetrahymena basal body centriole

EntireName: Transitional A-C linker of Tetrahymena basal body centriole
Components
  • Organelle or cellular component: Transitional A-C linker of Tetrahymena basal body centriole

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Supramolecule #1: Transitional A-C linker of Tetrahymena basal body centriole

SupramoleculeName: Transitional A-C linker of Tetrahymena basal body centriole
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 393606
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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