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- EMDB-52463: CryoEM structure of Asgard AtubA/B2 microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-52463
TitleCryoEM structure of Asgard AtubA/B2 microtubule
Map data
Sample
  • Complex: microtubule structure of Asgard tubulins AtubA/B2
    • Protein or peptide: Asgard tubulin AtubA with residues from TEV protease cleavage site
    • Protein or peptide: Asgard tubulin AtubB2
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsAsgard archaea / microtubule / cryoEM / cytomotive filaments / cytoskeleton / STRUCTURAL PROTEIN
Biological speciesCandidatus Lokiarchaeum ossiferum (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWollweber F / Xu J / Ponce-Toledo RI / Rodrigues-Oliveira T / Malit JJL / Kokhanovska A / Wieczorek M / 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
DepositionJan 7, 2025-
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_52463.png

Downloads & links

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Map

FileDownload / File: emd_52463.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 240 pix.
= 312. Å		1.3 Å/pix.
x 240 pix.
= 312. Å		1.3 Å/pix.
x 240 pix.
= 312. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.056935534 - 0.09229613
Average (Standard dev.)0.00080421317 (±0.005753073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52463_msk_1.map
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Half map: #1

Fileemd_52463_half_map_1.map
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Half map: #2

Fileemd_52463_half_map_2.map
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Sample components

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Entire : microtubule structure of Asgard tubulins AtubA/B2

EntireName: microtubule structure of Asgard tubulins AtubA/B2
Components
  • Complex: microtubule structure of Asgard tubulins AtubA/B2
    • Protein or peptide: Asgard tubulin AtubA with residues from TEV protease cleavage site
    • Protein or peptide: Asgard tubulin AtubB2
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: microtubule structure of Asgard tubulins AtubA/B2

SupramoleculeName: microtubule structure of Asgard tubulins AtubA/B2 / 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 AtubA with residues from TEV protease cleavage site

MacromoleculeName: Asgard tubulin AtubA with residues from TEV protease cleavage site
type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Lokiarchaeum ossiferum (archaea)
Molecular weightTheoretical: 46.706996 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 YRKLTEDAEN LYF

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Macromolecule #2: Asgard tubulin AtubB2

MacromoleculeName: Asgard tubulin AtubB2 / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Lokiarchaeum ossiferum (archaea)
Molecular weightTheoretical: 47.882949 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAREVITIHV GELGIQIAPN FWKYLCDEHN IDYKGQEKGK IRGVIDNFFE KASIGKWIPR TILVDLGPNA IRKVTKKDMK DFFDPKRCV MGLAGDANLF AKGYYSYGTR FMEEIMDKIQ KEVDQTEHLQ GFIVVHSIGD GTGAGLAPLI MEAIKKKHPK L VMMSYSIV ...String:
MAREVITIHV GELGIQIAPN FWKYLCDEHN IDYKGQEKGK IRGVIDNFFE KASIGKWIPR TILVDLGPNA IRKVTKKDMK DFFDPKRCV MGLAGDANLF AKGYYSYGTR FMEEIMDKIQ KEVDQTEHLQ GFIVVHSIGD GTGAGLAPLI MEAIKKKHPK L VMMSYSIV PSQNMDCSTI LPYNAILSLD KLTSCADISM IIDNDSIYRI VATQGKENEL SESIFDQVLA KALVEITATL RF NSPLNRS MMEMSTNLVP FPRNHFLMTS MSPLETSLTS AHQKIETKEL MQDLIDQDHI LAPITVEKGV FTAFVIALRG ENP HSILQN SIKGFGDRVK FSEIFPTAIK ADSTTLTDEK LARSGITLMN HSGVANLFQF LLTQFELMYD HDAFTTWYYQ EGMQ PSEFE AAKNNIQKLI TEYKQDEY

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Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 14 / 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 statefilament

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS 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

Final reconstructionApplied symmetry - Helical parameters - Δz: 11.73 Å
Applied symmetry - Helical parameters - Δ&Phi: 52.49 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39838
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Details: the initial model is generated from sub-tomogram average.
Final angle assignmentType: NOT APPLICABLE

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