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 9HXC | pdb_00009hxc

CryoEM structure of Asgard AtubA/B2 microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 9HXC

This is version 1.1 of the entry. See complete history. 

Literature

Microtubules in Asgard archaea.

Wollweber, F., Xu, J., Ponce-Toledo, R.I., Marxer, F., Rodrigues-Oliveira, T., Possnecker, A., Luo, Z.H., Malit, J.J.L., Kokhanovska, A., Wieczorek, M., Schleper, C., Pilhofer, M.

(2025) Cell 188: 2451

  • DOI: https://doi.org/10.1016/j.cell.2025.02.027
  • Primary Citation Related Structures: 
    9F6T, 9F6U, 9F6V, 9HXC

  • PubMed 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 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.


  • Organizational Affiliation: 
    • Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 1,330.46 kDa 
  • Atom Count: 93,142 
  • Modeled Residue Count: 11,886 
  • Deposited Residue Count: 11,914 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Asgard tubulin AtubA with residues from TEV protease cleavage site428Candidatus Lokiarchaeum ossiferumMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Asgard tubulin AtubB2423Candidatus Lokiarchaeum ossiferumMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
(Subject of Investigation/LOI)

Query on GDP



Download:Ideal Coordinates CCD File
CA [auth A]
DA [auth B]
EA [auth E]
FA [auth G]
GA [auth I]
CA [auth A],
DA [auth B],
EA [auth E],
FA [auth G],
GA [auth I],
HA [auth K],
IA [auth M],
JA [auth O],
KA [auth Q],
LA [auth S],
MA [auth U],
NA [auth W],
OA [auth Y],
PA [auth a]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101000232

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Data collection, Database references