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- EMDB-53454: Singlet microtubule after masked refinement. -

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Basic information

Entry
Database: EMDB / ID: EMD-53454
TitleSinglet microtubule after masked refinement.
Map data
Sample
  • Complex: microtubule assembled by MAP6d1
Keywordsmicrotubule / neuron / protein / CELL CYCLE
Biological speciesBos taurus (domestic cattle)
Methodsubtomogram averaging / cryo EM / Resolution: 12.5 Å
AuthorsGOPAL D / Wu J / Delaroche J / Bosc C / De Andrade M / Denarier E / Effantin G / Andrieux A / Gory-Faure S / Serre L / Arnal I
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Nat Commun / Year: 2025
Title: The Mn-motif protein MAP6d1 assembles ciliary doublet microtubules.
Authors: Dharshini Gopal / Juliette Wu / Julie Delaroche / Christophe Bosc / Manon De Andrade / Eric Denarier / Gregory Effantin / Annie Andrieux / Sylvie Gory-Fauré / Laurence Serre / Isabelle Arnal /
Abstract: Most eukaryotic cells have cilia that serve vital functions in sensing, signalling, motility. The core architecture of cilia is an array of microtubule doublets, which consist of a complete A-tubule ...Most eukaryotic cells have cilia that serve vital functions in sensing, signalling, motility. The core architecture of cilia is an array of microtubule doublets, which consist of a complete A-tubule and an incomplete B-tubule. How these structures assemble remains poorly understood. Using total internal reflection fluorescence microscopy and cryo-electron tomography, we investigate the role of MAP6d1, a brain-specific protein containing microtubule lumen-targeting Mn-motifs. We show that MAP6d1 assembles stable microtubule doublets by recruiting tubulin dimers onto the A-tubule lattice to initiate B-tubule nucleation. MAP6d1 also promotes the formation of luminal protofilaments in singlet and doublet microtubules, a previously undescribed phenomenon that likely enhances microtubule stability. In neurons, MAP6d1 localises to the proximal part of primary cilia via its Mn-motif, with its loss resulting in shortened cilia, a characteristic of ciliopathies. MAP6d1 is thus a neuronal Mn-motif protein with a specific role in assembling microtubule doublets and regulating ciliary length.
History
DepositionApr 18, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53454.png

Downloads & links

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Map

FileDownload / File: emd_53454.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 192 pix.
= 518.4 Å		2.7 Å/pix.
x 192 pix.
= 518.4 Å		2.7 Å/pix.
x 192 pix.
= 518.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1750.0
Minimum - Maximum0.0 - 4094.0
Average (Standard dev.)1651.550500000000056 (±369.339999999999975)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 518.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53454_msk_1.map
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Half map: #1

Fileemd_53454_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_53454_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : microtubule assembled by MAP6d1

EntireName: microtubule assembled by MAP6d1
Components
  • Complex: microtubule assembled by MAP6d1

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Supramolecule #1: microtubule assembled by MAP6d1

SupramoleculeName: microtubule assembled by MAP6d1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (domestic cattle)

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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: 6.7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.87 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 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: 12.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 5881
ExtractionNumber tomograms: 252 / Number images used: 5881
CTF correctionSoftware - Name: EMAN2 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: NOT APPLICABLE

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