7F1B

Odinarchaeota tubulin H393D mutant, in a pseudo protofilament arrangement, after GTP hydrolysis and phosphate release


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution.

Akil, C.Ali, S.Tran, L.T.Gaillard, J.Li, W.Hayashida, K.Hirose, M.Kato, T.Oshima, A.Fujishima, K.Blanchoin, L.Narita, A.Robinson, R.C.

(2022) Sci Adv 8: eabm2225-eabm2225

  • DOI: https://doi.org/10.1126/sciadv.abm2225
  • Primary Citation of Related Structures:  
    7EVB, 7EVC, 7EVD, 7EVE, 7EVG, 7EVH, 7EVI, 7EVK, 7EVL, 7F1A, 7F1B

  • PubMed Abstract: 

    Tubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea are the closest known prokaryotic relatives to eukaryotes. Here, we elucidated the apo and nucleotide-bound x-ray structures of an Asgard tubulin from hydrothermal living Odinarchaeota (OdinTubulin). The guanosine 5'-triphosphate (GTP)-bound structure resembles a microtubule protofilament, with GTP bound between subunits, coordinating the "+" end subunit through a network of water molecules and unexpectedly by two cations. A water molecule is located suitable for GTP hydrolysis. Time course crystallography and electron microscopy revealed conformational changes on GTP hydrolysis. OdinTubulin forms tubules at high temperatures, with short curved protofilaments coiling around the tubule circumference, more similar to FtsZ, rather than running parallel to its length, as in microtubules. Thus, OdinTubulin represents an evolutionary stage intermediate between prokaryotic FtsZ and eukaryotic microtubule-forming tubulins.


  • Organizational Affiliation

    Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin-like protein425Candidatus Odinarchaeum yellowstoniiMutation(s): 1 
Gene Names: cetZOdinLCB4_01330
UniProt
Find proteins for A0A1Q9N9N5 (Odinarchaeota yellowstonii (strain LCB_4))
Explore A0A1Q9N9N5 
Go to UniProtKB:  A0A1Q9N9N5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Q9N9N5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.883α = 90
b = 94.428β = 90
c = 100.846γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJCR19S5
Japan Society for the Promotion of Science (JSPS)JapanJP20H00476
Other privateUnited StatesMoore Simons Foundation GBMF9743

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description