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- EMDB-56153: Cryo-EM structure of AtubAB mini microtubules from Heimdallarchaeia -

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Basic information

Entry
Database: EMDB / ID: EMD-56153
TitleCryo-EM structure of AtubAB mini microtubules from Heimdallarchaeia
Map dataHelical map
Sample
  • Complex: AtubAB mini microtubule
    • Protein or peptide: AtubA
    • Protein or peptide: AtubB
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsMicrotubules / BtubAB / cytoskeleton / asgard archaea / eukaryogenesis / UNKNOWN FUNCTION
Biological speciesCandidatus Heimdallarchaeota archaeon (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLowe J / von Kugelgen A
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
Wellcome Trust203276/C/16/Z United Kingdom
Wellcome Trust227876/Z/23/Z United Kingdom
Wellcome Trust227452/Z/23/Z United Kingdom
CitationJournal: To Be Published
Title: Asgard archaeal AtubAB tubulins form mini microtubules exhibiting dynamic instability
Authors: Lowe J / von Kugelgen A
History
DepositionDec 22, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56153.png

Downloads & links

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Map

FileDownload / File: emd_56153.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 256 pix.
= 325.12 Å		1.27 Å/pix.
x 256 pix.
= 325.12 Å		1.27 Å/pix.
x 256 pix.
= 325.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027
Minimum - Maximum-0.07675266 - 0.1288521
Average (Standard dev.)0.00008549206 (±0.0074032363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 325.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56153_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_56153_msk_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D classification of heterodimer

Fileemd_56153_additional_1.map
Annotation3D classification of heterodimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_56153_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_56153_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AtubAB mini microtubule

EntireName: AtubAB mini microtubule
Components
  • Complex: AtubAB mini microtubule
    • Protein or peptide: AtubA
    • Protein or peptide: AtubB
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: AtubAB mini microtubule

SupramoleculeName: AtubAB mini microtubule / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon (archaea)
Molecular weightTheoretical: 94 kDa/nm

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Macromolecule #1: AtubA

MacromoleculeName: AtubA / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon (archaea)
Molecular weightTheoretical: 48.279441 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSEVVVVAVG QAGNQIADQF WQLIAQEHKI GLDGMPTNGE PTGRTDVFFR KVSNRYVPRA VLVDLEPAVL KSVSDDAKPN FYDPKNKVH GADGAGNNFA VGHTEMGAQY LEQVIGKIKN EVEKTDSLGG FIVTHSVGGG TGSGFGTLIM QNIRKEYPNT P LLSFSIYP ...String:
MSEVVVVAVG QAGNQIADQF WQLIAQEHKI GLDGMPTNGE PTGRTDVFFR KVSNRYVPRA VLVDLEPAVL KSVSDDAKPN FYDPKNKVH GADGAGNNFA VGHTEMGAQY LEQVIGKIKN EVEKTDSLGG FIVTHSVGGG TGSGFGTLIM QNIRKEYPNT P LLSFSIYP SPRISDVLTE PYNAIFSSYR LVRDTSCSII YDNDALYTIC QNLGIAEPTY SDLNKLISQS MVNITAGMRF VG TLNLDLR KLITNLVPHP RLHFLMTSTA PLVESGGFDS QSIEKTAEVL FEKSNIQAQV NTEDGAYIST TVLFRGNVNP ADM DTALRA MKQKLKFVSF IPTGFKTGLS ATAPNNMEFA AALVANHTGI TQVFKRILGQ FDKLWSRKAF SHWYTDSGLT EEDI VNARN DIAKLVEEYE ETLKFKSKDK SGEEVAAAEI AENK

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Macromolecule #2: AtubB

MacromoleculeName: AtubB / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon (archaea)
Molecular weightTheoretical: 46.27507 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 #3: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 16 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 6.9
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 10.248 Å
Applied symmetry - Helical parameters - Δ&Phi: -89.824 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 61534
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9tqk:
Cryo-EM structure of AtubAB mini microtubules from Heimdallarchaeia

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