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- EMDB-50565: 96nm repeat of the axonemal doublets from the tubulin glycylation... -

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Basic information

Entry
Database: EMDB / ID: EMD-50565
Title96nm repeat of the axonemal doublets from the tubulin glycylation depleted ttll3 strain from C.reinhardtii
Map data96nm repeat of the axonemal doublets from the ttll3 strain from C.reinhardtii
Sample
  • Organelle or cellular component: isolated axonemes from ttll3 C.reinhardtii cells
KeywordsCilia / axoneme / microtubule doublets / tubulin / STRUCTURAL PROTEIN
Biological speciesC.reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
AuthorsAlvarez Viar G / Pigino G
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)819826European Union
CitationJournal: Curr Biol / Year: 2024
Title: Protofilament-specific nanopatterns of tubulin post-translational modifications regulate the mechanics of ciliary beating.
Authors: Gonzalo Alvarez Viar / Nikolai Klena / Fabrizio Martino / Adrian Pascal Nievergelt / Davide Bolognini / Paola Capasso / Gaia Pigino /
Abstract: Controlling ciliary beating is essential for motility and signaling in eukaryotes. This process relies on the regulation of various axonemal proteins that assemble in stereotyped patterns onto ...Controlling ciliary beating is essential for motility and signaling in eukaryotes. This process relies on the regulation of various axonemal proteins that assemble in stereotyped patterns onto individual microtubules of the ciliary structure. Additionally, each axonemal protein interacts exclusively with determined tubulin protofilaments of the neighboring microtubule to carry out its function. While it is known that tubulin post-translational modifications (PTMs) are important for proper ciliary motility, the mode and extent to which they contribute to these interactions remain poorly understood. Currently, the prevailing understanding is that PTMs can confer functional specialization at the level of individual microtubules. However, this paradigm falls short of explaining how the tubulin code can manage the complexity of the axonemal structure where functional interactions happen in defined patterns at the sub-microtubular scale. Here, we combine immuno-cryo-electron tomography (cryo-ET), expansion microscopy, and mutant analysis to show that, in motile cilia, tubulin glycylation and polyglutamylation form mutually exclusive protofilament-specific nanopatterns at a sub-microtubular scale. These nanopatterns are consistent with the distributions of axonemal dyneins and nexin-dynein regulatory complexes, respectively, and are indispensable for their regulation during ciliary beating. Our findings offer a new paradigm for understanding how different tubulin PTMs, such as glycylation, glutamylation, acetylation, tyrosination, and detyrosination, can coexist within the ciliary structure and specialize individual protofilaments for the regulation of diverse protein complexes. The identification of a ciliary tubulin nanocode by cryo-ET suggests the need for high-resolution studies to better understand the molecular role of PTMs in other cellular compartments beyond the cilium.
History
DepositionJun 7, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50565.png

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Map

FileDownload / File: emd_50565.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation96nm repeat of the axonemal doublets from the ttll3 strain from C.reinhardtii
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.42 Å/pix.
x 140 pix.
= 1319.08 Å		9.42 Å/pix.
x 140 pix.
= 1319.08 Å		9.42 Å/pix.
x 140 pix.
= 1319.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 9.422 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 71.599999999999994
Minimum - Maximum63.558776999999999 - 77.73169
Average (Standard dev.)69.994519999999994 (±0.963426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 1319.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 of the 96nm repeat of...

Fileemd_50565_half_map_1.map
AnnotationHalf map 1 of the 96nm repeat of the axonemal doublets from the ttll3 strain from C.reinhardtii
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of the 96nm repeat of...

Fileemd_50565_half_map_2.map
AnnotationHalf map 2 of the 96nm repeat of the axonemal doublets from the ttll3 strain from C.reinhardtii
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : isolated axonemes from ttll3 C.reinhardtii cells

EntireName: isolated axonemes from ttll3 C.reinhardtii cells
Components
  • Organelle or cellular component: isolated axonemes from ttll3 C.reinhardtii cells

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Supramolecule #1: isolated axonemes from ttll3 C.reinhardtii cells

SupramoleculeName: isolated axonemes from ttll3 C.reinhardtii cells / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: C.reinhardtii (plant)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 7.22
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm

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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 / Number subtomograms used: 1016
ExtractionNumber tomograms: 3 / Number images used: 1016
Final angle assignmentType: OTHER / Details: cross correlation

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