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- EMDB-50240: cryoEM structure of Asgard tubulin heterodimer AtubA/B with GDP -

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Basic information

Entry
Database: EMDB / ID: EMD-50240
TitlecryoEM structure of Asgard tubulin heterodimer AtubA/B with GDP
Map data
Sample
  • Complex: Asgard tubulin heterodimer AtubA/B from Candidatus Lokiarchaeum ossiferum
    • Protein or peptide: Asgard tubulin A (AtubA) from Candidatus Lokiarchaeum ossiferum
    • Protein or peptide: Asgard tubulin B (AtubB) from Candidatus Lokiarchaeum ossiferum
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordscryoEM / tubulin / Asgard archaea / microtubule / CYTOSOLIC PROTEIN
Biological speciesCandidatus Lokiarchaeum ossiferum (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWollweber F / Xu J / Ponce-Toled RI / Rodrigues-Oliveira T / Malit JJL / Kokhanovska A / Schleper C / Pilhofer M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101000232European Union
CitationJournal: Cell / Year: 2025
Title: Microtubules in Asgard archaea.
Authors: Florian Wollweber / Jingwei Xu / Rafael I Ponce-Toledo / Florina Marxer / Thiago Rodrigues-Oliveira / Anja Pössnecker / Zhen-Hao Luo / Jessie James Limlingan Malit / Anastasiia Kokhanovska ...Authors: Florian Wollweber / Jingwei Xu / Rafael I Ponce-Toledo / Florina Marxer / Thiago Rodrigues-Oliveira / Anja Pössnecker / Zhen-Hao Luo / Jessie James Limlingan Malit / Anastasiia Kokhanovska / Michal Wieczorek / Christa Schleper / Martin Pilhofer /
Abstract: Microtubules are a hallmark of eukaryotes. Archaeal and bacterial homologs of tubulins typically form homopolymers and non-tubular superstructures. The origin of heterodimeric tubulins assembling ...Microtubules are a hallmark of eukaryotes. Archaeal and bacterial homologs of tubulins typically form homopolymers and non-tubular superstructures. The origin of heterodimeric tubulins assembling into microtubules remains unclear. Here, we report the discovery of microtubule-forming tubulins in Asgard archaea, the closest known relatives of eukaryotes. These Asgard tubulins (AtubA/B) are closely related to eukaryotic α/β-tubulins and the enigmatic bacterial tubulins BtubA/B. Proteomics of Candidatus Lokiarchaeum ossiferum showed that AtubA/B were highly expressed. Cryoelectron microscopy structures demonstrate that AtubA/B form eukaryote-like heterodimers, which assembled into 5-protofilament bona fide microtubules in vitro. The additional paralog AtubB2 lacks a nucleotide-binding site and competitively displaced AtubB. These AtubA/B2 heterodimers polymerized into 7-protofilament non-canonical microtubules. In a sub-population of Ca. Lokiarchaeum ossiferum cells, cryo-tomography revealed tubular structures, while expansion microscopy identified AtubA/B cytoskeletal assemblies. Our findings suggest a pre-eukaryotic origin of microtubules and provide a framework for understanding the fundamental principles of microtubule assembly.
History
DepositionMay 2, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50240.png

Downloads & links

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Map

FileDownload / File: emd_50240.map.gz / Format: CCP4 / Size: 15.6 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.)
1.3 Å/pix.
x 160 pix.
= 208. Å		1.3 Å/pix.
x 160 pix.
= 208. Å		1.3 Å/pix.
x 160 pix.
= 208. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-4.3270793 - 6.1866193
Average (Standard dev.)0.0017105452 (±0.1610173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50240_msk_1.map
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Additional map: the map that was processed by DeepEMhancer.

Fileemd_50240_additional_1.map
Annotationthe map that was processed by DeepEMhancer.
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Half map: #1

Fileemd_50240_half_map_1.map
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Half map: #2

Fileemd_50240_half_map_2.map
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Sample components

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Entire : Asgard tubulin heterodimer AtubA/B from Candidatus Lokiarchaeum o...

EntireName: Asgard tubulin heterodimer AtubA/B from Candidatus Lokiarchaeum ossiferum
Components
  • Complex: Asgard tubulin heterodimer AtubA/B from Candidatus Lokiarchaeum ossiferum
    • Protein or peptide: Asgard tubulin A (AtubA) from Candidatus Lokiarchaeum ossiferum
    • Protein or peptide: Asgard tubulin B (AtubB) from Candidatus Lokiarchaeum ossiferum
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Asgard tubulin heterodimer AtubA/B from Candidatus Lokiarchaeum o...

SupramoleculeName: Asgard tubulin heterodimer AtubA/B from Candidatus Lokiarchaeum ossiferum
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Candidatus Lokiarchaeum ossiferum (archaea)

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Macromolecule #1: Asgard tubulin A (AtubA) from Candidatus Lokiarchaeum ossiferum

MacromoleculeName: Asgard tubulin A (AtubA) from Candidatus Lokiarchaeum ossiferum
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Lokiarchaeum ossiferum (archaea)
Molecular weightTheoretical: 46.040281 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAGEIVCIQV GQAGNQIAGA FWQKICAEHG IDPVNGKAID VVGDTDIFFN TIGDKYIPRA VVVDLEPAVV ENIREKFGTL FDPKSIVSG ADGAGNNFAI GFNEHGAETL EKVMQVVEQR VSETESIGGF ILTHSCGGGT GSGFGSKILK TIRERYPKVP I FTFSIFPS ...String:
MAGEIVCIQV GQAGNQIAGA FWQKICAEHG IDPVNGKAID VVGDTDIFFN TIGDKYIPRA VVVDLEPAVV ENIREKFGTL FDPKSIVSG ADGAGNNFAI GFNEHGAETL EKVMQVVEQR VSETESIGGF ILTHSCGGGT GSGFGSKILK TIRERYPKVP I FTFSIFPS PKISETVVEP YNAIMTLSNL IKYASCSIVL DNEALFSIAE KKLEVENPSL EDLNLIIAQV LTNVTASLRF SG TLNLDLG KLVTNLVPFS NLHFLMASTA PLVLAGKESY EKMTAKELSA QVFGDEYICA ACKPTTGRYL AASVLFRGAV KTS DVNEAM ATVKEQNSFV NWIPTGFKIS KSETSPKDSA LGVIMLGNNS EIVSVFERIG ANFDRLWSRK AFAHWFTDSG FEEK DLDDA RALVQKVIDD YRKLTEDA

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Macromolecule #2: Asgard tubulin B (AtubB) from Candidatus Lokiarchaeum ossiferum

MacromoleculeName: Asgard tubulin B (AtubB) from Candidatus Lokiarchaeum ossiferum
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Lokiarchaeum ossiferum (archaea)
Molecular weightTheoretical: 46.883527 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGREVIMLHV GQAGIQVGAM YWKQICAEHN LDHNGAPIGG DIKGDPDCFF MKASGGKYVP RALLIDLEPK VVRQVGNEQL PSFFDPKNL IHGLYGGANS FAKGYLGEGR DMIDNIMEQL KKEVAKCESL QGFIMTHAVG GGSGGGLGCL IMEKIKEEYP K KILWSYSI ...String:
MGREVIMLHV GQAGIQVGAM YWKQICAEHN LDHNGAPIGG DIKGDPDCFF MKASGGKYVP RALLIDLEPK VVRQVGNEQL PSFFDPKNL IHGLYGGANS FAKGYLGEGR DMIDNIMEQL KKEVAKCESL QGFIMTHAVG GGSGGGLGCL IMEKIKEEYP K KILWSYSI LPSPLLSDAV VEPYNAILSL DKMIQYTDET VVIDNHALFQ IVTKNMGIDD PIYDDLNHVI SQALSDITAS LR FKGSLNT DMKEFLVNLV PYPRSHFLMA SFAPMATAED RQYAKLTTSN LANALFEENY MMAAVDVTKG TFLACSLLFR GEN TAQDIT NALLDIKGRI KFSSFIPTGI KYGMTGTAPE GLERSGSALI NHTGVAEIFN RILAQFNLMF DKGAFLNWYE IEGM SKDDF AGARDNVQKL SDEYKRDEE

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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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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, 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

BufferpH: 6.8
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
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: INSILICO MODEL / In silico model: the model was generated from AtubA/B-GTP.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71297
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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