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- EMDB-52575: MAP6d1 assembles microtubule doublets -

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Basic information

Entry
Database: EMDB / ID: EMD-52575
TitleMAP6d1 assembles microtubule doublets
Map data
Sample
  • Complex: microtubule doublet assembled by MAP6d1
    • Protein or peptide: MAP6d1
    • Protein or peptide: A-tubulin
    • Protein or peptide: B-tubulin
Keywordsmicrotubule / doublet / neuron / cilia / CELL CYCLE
Biological speciesBos taurus (domestic cattle) / Mus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 16.0 Å
AuthorsGopal D / 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
DepositionJan 16, 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_52575.png

Downloads & links

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Map

FileDownload / File: emd_52575.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 208 pix.
= 561.6 Å		2.7 Å/pix.
x 208 pix.
= 561.6 Å		2.7 Å/pix.
x 208 pix.
= 561.6 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: 0.631
Minimum - Maximum-7.1363964 - 9.899409
Average (Standard dev.)0.16246502 (±1.0000008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-104-104-104
Dimensions208208208
Spacing208208208
CellA=B=C: 561.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52575_msk_1.map
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Half map: #1

Fileemd_52575_half_map_1.map
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Half map: #2

Fileemd_52575_half_map_2.map
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Sample components

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Entire : microtubule doublet assembled by MAP6d1

EntireName: microtubule doublet assembled by MAP6d1
Components
  • Complex: microtubule doublet assembled by MAP6d1
    • Protein or peptide: MAP6d1
    • Protein or peptide: A-tubulin
    • Protein or peptide: B-tubulin

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Supramolecule #1: microtubule doublet assembled by MAP6d1

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

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Macromolecule #1: MAP6d1

MacromoleculeName: MAP6d1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAWPCISRLC CLARRWNQLD RSDVAVPLTL HGYSDPGSEE SGADCSVSRG NPSVAGARES SRAVPLTQYQ RDFGVRTARA GSRDAAQERP SGPGGRRGQS SAPPTRTVYV LPVGDADAAV VATTSYRQEF QAWTGVKPSR STKARTARVV TTHSSGWDPS PGASFQVPEV ...String:
MAWPCISRLC CLARRWNQLD RSDVAVPLTL HGYSDPGSEE SGADCSVSRG NPSVAGARES SRAVPLTQYQ RDFGVRTARA GSRDAAQERP SGPGGRRGQS SAPPTRTVYV LPVGDADAAV VATTSYRQEF QAWTGVKPSR STKARTARVV TTHSSGWDPS PGASFQVPEV RKFTPNPSAI FQTSAPQTLN VGDPPVATHH HHHHHH

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Macromolecule #2: A-tubulin

MacromoleculeName: A-tubulin / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MRECISVHVG QAGVQMGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFT TFFCETGAGK HVPRAVFVD LEPTVIDEIR NGPYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDPVL D RIRKLSDQ CTGLQGFLVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE ...String:
MRECISVHVG QAGVQMGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFT TFFCETGAGK HVPRAVFVD LEPTVIDEIR NGPYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDPVL D RIRKLSDQ CTGLQGFLVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE FSIYPAPQVS TA VVEPYNS ILTTHTTLEH SDCAFMVDNE AIYDICRRNL DIERPTYTNL NRLISQIVSS ITA SLRFDG ALNVDLTEFQ TNLVPYPRIH FPLATYAPVI SAEKAYHEQL SVAEITNACF EPAN QMVKC DPRHGKYMAC CLLYRGDVVP KDVNAAIAAI KTKRSIQFVD WCPTGFKVGI NYQPP TVVP GGDLAKVQRA VCMLSNTTAI AEAWARLDHK FDLMYAKRAF VHWYVGEGME EGEFSE ARE DMAALEKDYE EVGIDSYEDE DEGEE

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Macromolecule #3: B-tubulin

MacromoleculeName: B-tubulin / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKEAESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVV ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKEAESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVV PSPKVSDTVV EPYNATLSVH QLVENTDETY CIDNEALYDI CFRTLKLTTP TYGDLNHLVS ATMSGVTTCL RFPGQLNADL RKLAVNMVPF PRLHFFMPGF APLTSRGSQQ YRALTVPELT QQVFDAKNMM AACDPRHGRY LTVAAVFRGR MSMKEVDEQM LNVQNKNSSY FVEWIPNNVK TAVCDIPPRG LKMAVTFIGN STAIQELFKR ISEQFTAMFR RKAFLHWYTG EGMDEMEFTE AESNMNDLVS EYQQYQDATA EEEEDFGEEA EEEA

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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: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 4997
ExtractionNumber tomograms: 252 / Number images used: 4997
CTF correctionSoftware - Name: EMAN2 / Details: CTF estimated by EMAN2 / Type: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: EMAN2

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