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- EMDB-52022: 96nm axonemal repeat of Chlamydomonas r. mutant IFT46-mNG VASHko ... -

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Basic information

Entry
Database: EMDB / ID: EMD-52022
Title96nm axonemal repeat of Chlamydomonas r. mutant IFT46-mNG VASHko lacking tubulin detyrosination
Map data96nm axonemal repeat of the Chlamydomonas r. mutant IFT46-mNG VASHko, which lacks tubulin detyrosination
Sample
  • Organelle or cellular component: isolated axoeneme from C. reinhardtii mutant IFT46-mNG VASHko
Keywordscilia / axoneme / tubulin / PTMs / detyrosination / STRUCTURAL PROTEIN
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 22.56 Å
AuthorsAlvarez Viar G / Pigino G
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)819826European Union
CitationJournal: Nat Commun / Year: 2025
Title: Tubulin tyrosination/detyrosination regulate the affinity and sorting of intraflagellar transport trains on axonemal microtubule doublets.
Authors: Aditya Chhatre / Ludek Stepanek / Adrian Pascal Nievergelt / Gonzalo Alvarez Viar / Stefan Diez / Gaia Pigino /
Abstract: Cilia assembly and function rely on the bidirectional transport of components between the cell body and ciliary tip via Intraflagellar Transport (IFT) trains. Anterograde and retrograde IFT trains ...Cilia assembly and function rely on the bidirectional transport of components between the cell body and ciliary tip via Intraflagellar Transport (IFT) trains. Anterograde and retrograde IFT trains travel along the B- and A-tubules of microtubule doublets, respectively, ensuring smooth traffic flow. However, the mechanism underlying this segregation remains unclear. Here, we test whether tubulin detyrosination (enriched on B-tubules) and tyrosination (enriched on A-tubules) have a role in IFT logistics. We report that knockout of tubulin detyrosinase VashL in Chlamydomonas reinhardtii causes frequent IFT train stoppages and impaired ciliary growth. By reconstituting IFT train motility on de-membranated axonemes and synthetic microtubules, we show that anterograde and retrograde trains preferentially associate with detyrosinated and tyrosinated microtubules, respectively. We propose that tubulin tyrosination/detyrosination is crucial for spatial segregation and collision-free IFT train motion, highlighting the significance of the tubulin code in ciliary transport.
History
DepositionNov 7, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52022.png

Downloads & links

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Map

FileDownload / File: emd_52022.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation96nm axonemal repeat of the Chlamydomonas r. mutant IFT46-mNG VASHko, which lacks tubulin detyrosination
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.28 Å/pix.
x 140 pix.
= 1579.2 Å		11.28 Å/pix.
x 140 pix.
= 1579.2 Å		11.28 Å/pix.
x 140 pix.
= 1579.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 11.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.98
Minimum - Maximum-25.329291999999999 - 33.858592999999999
Average (Standard dev.)-1.1719657 (±2.8996658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 1579.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 2

Fileemd_52022_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_52022_half_map_2.map
Annotationhalf map 1
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 axoeneme from C. reinhardtii mutant IFT46-mNG VASHko

EntireName: isolated axoeneme from C. reinhardtii mutant IFT46-mNG VASHko
Components
  • Organelle or cellular component: isolated axoeneme from C. reinhardtii mutant IFT46-mNG VASHko

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Supramolecule #1: isolated axoeneme from C. reinhardtii mutant IFT46-mNG VASHko

SupramoleculeName: isolated axoeneme from C. reinhardtii mutant IFT46-mNG VASHko
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: Lacks tubulin detyrosination
Source (natural)Organism: Chlamydomonas 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 2.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 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: 22.56 Å / Resolution method: OTHER
Details: We hit Nyquist at 11.28A pixel size (binned tomograms)
Number subtomograms used: 841
ExtractionNumber tomograms: 6 / Number images used: 841
Final angle assignmentType: OTHER / Details: Cross correlation coefficient (PEET software)

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