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- EMDB-69801: Averaged protofilament of Heimdallarchaeales alpha/beta tubulin m... -

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Basic information

Entry
Database: EMDB / ID: EMD-69801
TitleAveraged protofilament of Heimdallarchaeales alpha/beta tubulin microtubule with a single seam
Map dataThis map was derived from EMD-69786 by real-space averaging.
Sample
  • Complex: Averaged protofilament of Heimdallarchaeales alpha/beta tubulin microtubule with a single seam
    • Protein or peptide: Heim-alpha-tubulin
    • Protein or peptide: Heim-beta-tubulin
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsHeimdallarchaea tubulin microtubule archaea / PROTEIN FIBRIL
Biological speciesCandidatus Heimdallarchaeaceae (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsTran LT / Ali S / Matsumoto T / Yamazaki Y / Narita A / Miyazaki M / Robinson RC
Funding support Japan, 8 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25K18436 Japan
Japan Society for the Promotion of Science (JSPS)22H05171 Japan
Japan Society for the Promotion of Science (JSPS)23764079 Japan
Other private2025-4021 Japan
Other private Japan
Other private500230057 Japan
Japan Science and TechnologyJPMJFR2417 Japan
Other private Japan
CitationJournal: Sci Adv / Year: 2026
Title: Structure and dynamics of a four-protofilament microtubule from Heimdallarchaeales α/β-tubulin.
Authors: Linh T Tran / Samson Ali / Tomoharu Matsumoto / Yosuke Yamazaki / Akihiro Narita / Makito Miyazaki / Robert C Robinson /
Abstract: Eukaryotic microtubules are typically 13-protofilament tubes assembled from α/β-tubulin heterodimers that combine mechanical rigidity with dynamic instability. Homologous tubulins have been ...Eukaryotic microtubules are typically 13-protofilament tubes assembled from α/β-tubulin heterodimers that combine mechanical rigidity with dynamic instability. Homologous tubulins have been identified in Asgard archaea, the closest prokaryotic relatives to eukaryotes. Here, we characterize a heterodimeric α/β-tubulin system from Heimdallarchaeales. Biochemical reconstitution shows that α/β-tubulin forms a heterodimer that undergoes guanosine 5'-triphosphate-dependent polymerization with coupled nucleotide hydrolysis. Cryo-electron microscopy reveals that the polymers are composed of four-protofilament tubules, with microtubule-like lattices formed by conserved longitudinal interfaces and ball-and-socket lateral contacts. Single-filament imaging demonstrates intrinsic kinetic polarity and dynamic instability, while liposome encapsulation shows that microtubule growth generates forces sufficient to deform membranes. Despite their reduced protofilament number, -α/β-microtubules share key structural and dynamic features with eukaryotic microtubules but exhibit lower bending stiffness and polymerization force. Thus, microtubule-like polymers can form from a range of protofilament numbers, with reduced architectures potentially adapted to small cellular dimensions and lower mechanical loads. Together, our results indicate expansion in microtubule protofilament number during eukaryogenesis.
History
DepositionMar 19, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_69801.png

Downloads & links

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Map

FileDownload / File: emd_69801.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map was derived from EMD-69786 by real-space averaging.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 400 pix.
= 301.176 Å		0.75 Å/pix.
x 400 pix.
= 301.176 Å		0.75 Å/pix.
x 400 pix.
= 301.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75294 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.1580554 - 0.25663495
Average (Standard dev.)0.00012927137 (±0.0051984373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 301.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_69801_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_69801_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 : Averaged protofilament of Heimdallarchaeales alpha/beta tubulin m...

EntireName: Averaged protofilament of Heimdallarchaeales alpha/beta tubulin microtubule with a single seam
Components
  • Complex: Averaged protofilament of Heimdallarchaeales alpha/beta tubulin microtubule with a single seam
    • Protein or peptide: Heim-alpha-tubulin
    • Protein or peptide: Heim-beta-tubulin
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Averaged protofilament of Heimdallarchaeales alpha/beta tubulin m...

SupramoleculeName: Averaged protofilament of Heimdallarchaeales alpha/beta tubulin microtubule with a single seam
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Candidatus Heimdallarchaeaceae (archaea)

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Macromolecule #1: Heim-alpha-tubulin

MacromoleculeName: Heim-alpha-tubulin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Heimdallarchaeaceae (archaea)
Molecular weightTheoretical: 46.27507 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSREIISIHV GQAGLQVGAA FWRTVLEEHG LGNDGSVVDA SKEKSAVYFK QAGNNKFVPR AILVDLEPMV IKTIMNDLPG LFDPAYTIH GQSGAANNWA RGYRGADGEV NVDDVLKIVE KAVSETDSLQ GFSISHSIGG GTGSGLGSQI LKKLKETYPK Y PIITFSVF ...String:
MSREIISIHV GQAGLQVGAA FWRTVLEEHG LGNDGSVVDA SKEKSAVYFK QAGNNKFVPR AILVDLEPMV IKTIMNDLPG LFDPAYTIH GQSGAANNWA RGYRGADGEV NVDDVLKIVE KAVSETDSLQ GFSISHSIGG GTGSGLGSQI LKKLKETYPK Y PIITFSVF PSPLISDAVT EPYNSVFALD HLIEYADETI VLDNHALYNL TKNNMGIKSP SYADLNKIIS WVMSGVTASL RF KGDLNTD LKELLVNLVP FPRQHFLTST FSPIKNGTGS FEEVTTHDII NQLFDPNNAM SDTNFDEGAY IASVVMMRGH EVK TNAVNS SLAEIKGKLR FSEFIPTGIK TGVTSETLVG FESTGLNLSN HTGITKVFKR LAAQFDAMYE RDAFVHWYLG EGMS KDDME KARENLGKLT TEYDTSV

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Macromolecule #2: Heim-beta-tubulin

MacromoleculeName: Heim-beta-tubulin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Heimdallarchaeaceae (archaea)
Molecular weightTheoretical: 48.320492 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGEVVVVAV GQAGNQIADQ FWQLIAQEHK IGLDGMPTNG EPTGRTDVFF RKVSNRYVPR AVLVDLEPAV LKSVSDDAKP NFYDPKNKV HGADGAGNNF AVGHTEMGAQ YLEQVIGKIK NEVEKTDSLG GFIVTHSVGG GTGSGFGTLI MQNIRKEYPN T PLLSFSIY ...String:
MAGEVVVVAV GQAGNQIADQ FWQLIAQEHK IGLDGMPTNG EPTGRTDVFF RKVSNRYVPR AVLVDLEPAV LKSVSDDAKP NFYDPKNKV HGADGAGNNF AVGHTEMGAQ YLEQVIGKIK NEVEKTDSLG GFIVTHSVGG GTGSGFGTLI MQNIRKEYPN T PLLSFSIY PSPRISDVLT EPYNAIFSSY RLVRDTSCSI IYDNDALYTI CQNLGIAEPT YSDLNKLISQ SMVNITAGMR FV GTLNLDL RKLITNLVPH PRLHFLMTST APLVESGGFD SQSIEKTAEV LFEKSNIQAQ VNTEDGAYIS TTVLFRGNVN PAD MDTALR AMKQKLKFVS FIPTGFKTGL SATAPNNMEF AAALVANHTG ITQVFKRILG QFDKLWSRKA FSHWYTDSGL TEED IVNAR NDIAKLVEEY EETLKFKSKD KSGEEVAAAE IAENK

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Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration2.3 mg/mL
BufferpH: 6.8
Details: 100mM K-PIPES 10% glycerol 10 mM K-Phosphate 0.5 mM EGTA 0.5 mM MgSO4 2 mM GTP
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 4213 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 83.9 Å
Applied symmetry - Helical parameters - Δ&Phi: 0.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 223429
CTF correctionSoftware - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 2341375 / Software - Name: RELION (ver. 5.0)
Startup modelType of model: OTHER / Details: Empty cylinder generated by relion_helix_toolbox
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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