24SV | pdb_000024sv

Averaged protofilament of Heimdallarchaeales alpha/beta tubulin microtubule with a single seam


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 24SV

This is version 1.1 of the entry. See complete history

Literature

Structure and dynamics of a four-protofilament microtubule from Heimdallarchaeales alpha / beta-tubulin.

Tran, L.T.Ali, S.Matsumoto, T.Yamazaki, Y.Narita, A.Miyazaki, M.Robinson, R.C.

(2026) Sci Adv 12: eaeh4305-eaeh4305

  • DOI: https://doi.org/10.1126/sciadv.aeh4305
  • Primary Citation Related Structures: 
    24RT, 24SV, 24SW

  • PubMed Abstract: 

    Eukaryotic microtubules are typically 13-protofilament tubes assembled from α/β-tubulin heterodimers that combine mechanical rigidity with dynamic instability. Homologous tubulins have been identified in Asgard archaea, the closest prokaryotic relatives to eukaryotes. Here, we characterize a heterodimeric α/β-tubulin system from Heimdallarchaeales. Biochemical reconstitution shows that Heim- α/β-tubulin forms a heterodimer that undergoes guanosine 5'-triphosphate-dependent polymerization with coupled nucleotide hydrolysis. Cryo-electron microscopy reveals that the polymers are composed of four-protofilament tubules, with microtubule-like lattices formed by conserved longitudinal interfaces and ball-and-socket lateral contacts. Single-filament imaging demonstrates intrinsic kinetic polarity and dynamic instability, while liposome encapsulation shows that microtubule growth generates forces sufficient to deform membranes. Despite their reduced protofilament number, Heim -α/β-microtubules share key structural and dynamic features with eukaryotic microtubules but exhibit lower bending stiffness and polymerization force. Thus, microtubule-like polymers can form from a range of protofilament numbers, with reduced architectures potentially adapted to small cellular dimensions and lower mechanical loads. Together, our results indicate expansion in microtubule protofilament number during eukaryogenesis.


  • Organizational Affiliation
    • RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

Macromolecule Content 

  • Total Structure Weight: 191.06 kDa 
  • Atom Count: 13,112 
  • Modeled Residue Count: 1,682 
  • Deposited Residue Count: 1,724 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heim-alpha-tubulin
A, C
422Candidatus HeimdallarchaeaceaeMutation(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
Heim-beta-tubulin
B, D
440Candidatus HeimdallarchaeaceaeMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
(Subject of Investigation/LOI)

Query on GDP



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
L [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
K [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION5.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan25K18436
Japan Society for the Promotion of Science (JSPS)Japan22H05171
Japan Society for the Promotion of Science (JSPS)Japan23764079
Other privateJapan2025-4021
Other privateJapan--
Other privateJapan500230057
Japan Science and TechnologyJapanJPMJFR2417
Other privateJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-24
    Type: Initial release
  • Version 1.1: 2026-08-05
    Changes: Data collection, Database references