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- EMDB-53979: A-microtubule associated with Tetrahymena proximal A-C linker -

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Basic information

Entry
Database: EMDB / ID: EMD-53979
TitleA-microtubule associated with Tetrahymena proximal A-C linker
Map dataA-microtubule associated with proximal A-C linker, B-factor sharpened using relion_postprocess, original pixel size 1.34
Sample
  • Organelle or cellular component: proximal A-C linker of Tetrahymena thermophila basal body centriole
Keywordscentriole / basal body / centrosome / STRUCTURAL PROTEIN
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 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_53979.png

Downloads & links

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Map

FileDownload / File: emd_53979.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA-microtubule associated with proximal A-C linker, B-factor sharpened using relion_postprocess, original pixel size 1.34
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 360 pix.
= 482.4 Å		1.34 Å/pix.
x 360 pix.
= 482.4 Å		1.34 Å/pix.
x 360 pix.
= 482.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.014082559 - 0.01823444
Average (Standard dev.)0.00004907992 (±0.0010863631)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 482.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: A-microtubule associated with proximal A-C linker, B-factor sharpened...

Fileemd_53979_additional_1.map
AnnotationA-microtubule associated with proximal A-C linker, B-factor sharpened using relion_postprocess, pixel size corrected to 1.315
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: A-microtubule associated with proximal A-C linker, processed with...

Fileemd_53979_additional_2.map
AnnotationA-microtubule associated with proximal A-C linker, processed with EMReady, pixel size corrected to 1.315
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53979_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53979_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : proximal A-C linker of Tetrahymena thermophila basal body centriole

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

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

SupramoleculeName: proximal A-C linker of Tetrahymena thermophila basal body centriole
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#27
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: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41701
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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