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- EMDB-56152: Cryo-EM structure of AtubAB heterodimer from Heimdallarchaeia -

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Basic information

Entry
Database: EMDB / ID: EMD-56152
TitleCryo-EM structure of AtubAB heterodimer from Heimdallarchaeia
Map dataCryo-EM map of AtubAB heterodimer
Sample
  • Complex: AtubAB heterodimer
    • 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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_56152.png

Downloads & links

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Map

FileDownload / File: emd_56152.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of AtubAB heterodimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 210 pix.
= 200.55 Å		0.96 Å/pix.
x 210 pix.
= 200.55 Å		0.96 Å/pix.
x 210 pix.
= 200.55 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.955 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0191
Minimum - Maximum-0.06254549 - 0.10618052
Average (Standard dev.)0.000033297136 (±0.003586541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 200.55 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56152_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_56152_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_56152_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 heterodimer

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

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Supramolecule #1: AtubAB heterodimer

SupramoleculeName: AtubAB heterodimer / 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: 1 / 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: 1 / 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: 1 / 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.7
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: 50.0 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 125647
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9tqj:
Cryo-EM structure of AtubAB heterodimer from Heimdallarchaeia

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