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TitleStructure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution.
Journal, issue, pagesSci Adv, Vol. 8, Issue 12, Page eabm2225, Year 2022
Publish dateMar 25, 2022
AuthorsCaner Akıl / Samson Ali / Linh T Tran / Jérémie Gaillard / Wenfei Li / Kenichi Hayashida / Mika Hirose / Takayuki Kato / Atsunori Oshima / Kosuke Fujishima / Laurent Blanchoin / Akihiro Narita / Robert C Robinson /
PubMed AbstractTubulins 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 ...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.
External linksSci Adv / PubMed:35333570 / PubMed Central
MethodsEM (helical sym.) / X-ray diffraction
Resolution1.25 - 37.17 Å
Structure data

EMDB-32629: Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution
Method: EM (helical sym.) / Resolution: 37.17 Å

EMDB-32630: Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution
Method: EM (helical sym.) / Resolution: 28.82 Å

PDB-7evb:
Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 77% GTP/23% and 2 Na+
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-7evc:
Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 60% GTP/40% GDP and 2 Na+
Method: X-RAY DIFFRACTION / Resolution: 1.25 Å

PDB-7evd:
Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 53% GTP/47% and 2 Na+
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-7eve:
Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 100% GDP and 2 Na+
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-7evg:
Apo Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a psuedo-protofilament arrangement
Method: X-RAY DIFFRACTION / Resolution: 2.48 Å

PDB-7evh:
Odinarchaeota tubulin H393D mutant, in a psuedo protofilament arrangement, bound to 59% GDP, 41% phosphate
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-7evi:
Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 79% GTP, 21% GDP, Na+, Mg2+
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-7evk:
Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 78% GTP, 22% GDP, Na+
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7evl:
Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 64% GTP/36% GDP and 2 Na+ in a small unit cell
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-7f1a:
Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound 78% GTP/22% GDP 1 K+, 1 Mg2+
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7f1b:
Odinarchaeota tubulin H393D mutant, in a pseudo protofilament arrangement, after GTP hydrolysis and phosphate release
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

Chemicals

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER / Water

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

Source
  • Candidatus Odinarchaeota archaeon LCB_4 (archaea)
  • odinarchaeota archaeon (strain lcb_4) (archaea)
KeywordsSTRUCTURAL PROTEIN / Asgard / tubulin / GTP / filament

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