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- PDB-9f6u: cryoEM structure of Asgard tubulin heterodimer AtubA/B with GDP -

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Basic information

Entry
Database: PDB / ID: 9f6u
TitlecryoEM structure of Asgard tubulin heterodimer AtubA/B with GDP
Components
  • Asgard tubulin A (AtubA) from Candidatus Lokiarchaeum ossiferum
  • Asgard tubulin B (AtubB) from Candidatus Lokiarchaeum ossiferum
KeywordsCYTOSOLIC PROTEIN / cryoEM / tubulin / Asgard archaea / microtubule
Function / homologyGUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesCandidatus Lokiarchaeum ossiferum (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWollweber, F. / Xu, J. / Ponce-Toled, R.I. / Rodrigues-Oliveira, T. / Malit, J.J.L. / Kokhanovska, A. / Schleper, C. / Pilhofer, M.
Funding supportEuropean Union, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Asgard tubulin A (AtubA) from Candidatus Lokiarchaeum ossiferum
B: Asgard tubulin B (AtubB) from Candidatus Lokiarchaeum ossiferum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8904
Polymers92,9242
Non-polymers9662
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 46040.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Lokiarchaeum ossiferum (archaea)
Production host: Spodoptera frugiperda (fall armyworm)
#2: Protein Asgard tubulin B (AtubB) from Candidatus Lokiarchaeum ossiferum


Mass: 46883.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Lokiarchaeum ossiferum (archaea)
Production host: Spodoptera frugiperda (fall armyworm)
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Asgard tubulin heterodimer AtubA/B from Candidatus Lokiarchaeum ossiferum
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Candidatus Lokiarchaeum ossiferum (archaea)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71297 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0186700
ELECTRON MICROSCOPYf_angle_d1.5499076
ELECTRON MICROSCOPYf_dihedral_angle_d11.9452452
ELECTRON MICROSCOPYf_chiral_restr0.0771017
ELECTRON MICROSCOPYf_plane_restr0.0081169

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