8OUK | pdb_00008ouk

Arf GTPase from the asgard Hodarchaea : HodArfR1 bound to GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.215 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The Asgard archaeal origins of Arf family GTPases involved in eukaryotic organelle dynamics.

Vargova, R.Chevreau, R.Alves, M.Courbin, C.Terry, K.Legrand, P.Elias, M.Menetrey, J.Dacks, J.B.Jackson, C.L.

(2025) Nat Microbiol 10: 495-508

  • DOI: https://doi.org/10.1038/s41564-024-01904-6
  • Primary Citation of Related Structures:  
    8OUK, 8OUL, 8OUM, 8OUN

  • PubMed Abstract: 

    The evolution of eukaryotes is a fundamental event in the history of life. The closest prokaryotic lineage to eukaryotes, the Asgardarchaeota, encode proteins previously found only in eukaryotes, providing insight into their archaeal ancestor. Eukaryotic cells are characterized by endomembrane organelles, and the Arf family GTPases regulate organelle dynamics by recruiting effector proteins to membranes upon activation. The Arf family is ubiquitous among eukaryotes, but its origins remain elusive. Here we report a group of prokaryotic GTPases, the ArfRs, which are widely present in Asgardarchaeota. Phylogenetic analyses reveal that eukaryotic Arf family proteins arose from the ArfR group. Expression of representative Asgardarchaeota ArfR proteins in yeast and X-ray crystallographic studies show that ArfR GTPases possess the mechanism of membrane binding and structural features unique to Arf family proteins. Our results indicate that Arf family GTPases originated in the archaeal ancestor of eukaryotes, consistent with aspects of the endomembrane system evolving early in eukaryogenesis.


  • Organizational Affiliation
    • Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arf GTPase179PromethearchaeatiMutation(s): 1 
Gene Names: OLS23013
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.215 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.12α = 90
b = 59.12β = 90
c = 119.73γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-20-CE13-0007-02

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Database references, Structure summary
  • Version 1.2: 2025-02-12
    Changes: Database references