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- EMDB-52574: MAP6d1 assembles microtubule doublets -

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Basic information

Entry
Database: EMDB / ID: EMD-52574
TitleMAP6d1 assembles microtubule doublets
Map data
Sample
  • Complex: B-tubule of 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: 22.0 Å
AuthorsGopal D / Serre L / Arnal I
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: The Mn-motif protein MAP6d1 assembles ciliary doublet microtubules
Authors: Gopal D / Wu J / Delaroche J / Bosc C / De Andrade M / Denarier E / Effantin G / Andrieux A / Gory-Faure S / Serre L / Arnal I
History
DepositionJan 16, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52574.png

Downloads & links

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Map

FileDownload / File: emd_52574.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2130.0
Minimum - Maximum1.0 - 4095.0
Average (Standard dev.)1749.531700000000001 (±255.754899999999992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
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_52574_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52574_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52574_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : B-tubule of microtubule doublet assembled by MAP6d1

EntireName: B-tubule of microtubule doublet assembled by MAP6d1
Components
  • Complex: B-tubule of 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: B-tubule of microtubule doublet assembled by MAP6d1

SupramoleculeName: B-tubule of 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: 22.0 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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