8OUM | pdb_00008oum

Arf GTPase from the asgard Gerdarchaea : GerdArfR1 bound to GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 
    0.267 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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
GTP-binding protein
A, B, C, D, E
178Promethearchaeati archaeonMutation(s): 1 
Gene Names: FK733_07565
UniProt
Find proteins for A0A8J7ZFD1 (Promethearchaeati archaeon)
Explore A0A8J7ZFD1 
Go to UniProtKB:  A0A8J7ZFD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8J7ZFD1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D],
N [auth E]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free:  0.267 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.25α = 90
b = 54.88β = 94.47
c = 121.79γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASESphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

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