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- EMDB-52469: Sub-tomogram average of Asgard AtubA/B microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-52469
TitleSub-tomogram average of Asgard AtubA/B microtubule
Map data
Sample
  • Complex: microtubule structure of Asgard tubulins AtubA/B
KeywordsAsgard archaea / microtubule / cryoEM / cytomotive filaments / cytoskeleton / STRUCTURAL PROTEIN
Biological speciesCandidatus Lokiarchaeum ossiferum (archaea)
Methodsubtomogram averaging / cryo EM / Resolution: 18.0 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_52469.png

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Map

FileDownload / File: emd_52469.map.gz / Format: CCP4 / Size: 686.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
8 Å/pix.
x 56 pix.
= 448. Å		8 Å/pix.
x 56 pix.
= 448. Å		8 Å/pix.
x 56 pix.
= 448. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 8 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-1.0113052 - 2.1626775
Average (Standard dev.)0.08116847 (±0.3207387)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions565656
Spacing565656
CellA=B=C: 448.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52469_msk_1.map
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Half map: #1

Fileemd_52469_half_map_1.map
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Half map: #2

Fileemd_52469_half_map_2.map
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Sample components

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Entire : microtubule structure of Asgard tubulins AtubA/B

EntireName: microtubule structure of Asgard tubulins AtubA/B
Components
  • Complex: microtubule structure of Asgard tubulins AtubA/B

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

SupramoleculeName: microtubule structure of Asgard tubulins AtubA/B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Candidatus Lokiarchaeum ossiferum (archaea)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
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: 4.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 2363
ExtractionNumber tomograms: 36 / Number images used: 4264
CTF correctionType: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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