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Yorodumi- PDB-7f1a: Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f1a | ||||||||||||
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Title | Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound 78% GTP/22% GDP 1 K+, 1 Mg2+ | ||||||||||||
Components | Tubulin-like protein | ||||||||||||
Keywords | STRUCTURAL PROTEIN / Asgard / tubulin / GTP / filament | ||||||||||||
Function / homology | Function and homology information microtubule-based process / structural constituent of cytoskeleton / microtubule / GTPase activity / GTP binding Similarity search - Function | ||||||||||||
Biological species | Odinarchaeota archaeon | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | Robinson, R.C. / Akil, C. / Tran, L.T. | ||||||||||||
Funding support | Japan, United States, 3items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution. Authors: Caner Akıl / Samson Ali / Linh T Tran / Jérémie Gaillard / Wenfei Li / Kenichi Hayashida / Mika Hirose / Takayuki Kato / Atsunori Oshima / Kosuke Fujishima / Laurent Blanchoin / Akihiro ...Authors: Caner 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 / 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 ...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. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f1a.cif.gz | 198.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f1a.ent.gz | 148.5 KB | Display | PDB format |
PDBx/mmJSON format | 7f1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f1a_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7f1a_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7f1a_validation.xml.gz | 19 KB | Display | |
Data in CIF | 7f1a_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/7f1a ftp://data.pdbj.org/pub/pdb/validation_reports/f1/7f1a | HTTPS FTP |
-Related structure data
Related structure data | 7evbSC 7evcC 7evdC 7eveC 7evgC 7evhC 7eviC 7evkC 7evlC 7f1bC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules B
#1: Protein | Mass: 47633.406 Da / Num. of mol.: 1 / Mutation: H393D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Odinarchaeota archaeon (strain LCB_4) (archaea) Strain: LCB_4 / Gene: cetZ, OdinLCB4_01330 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9N9N5 |
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-Non-polymers , 5 types, 180 molecules
#2: Chemical | ChemComp-GTP / |
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#3: Chemical | ChemComp-GDP / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-K / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 25% PEG 1500 0.1 M MMT (1 DL-malic acid: 2 MES: 2 Tris base), pH 9.0 Soak: 10 mM GTP, 1 mM MgCl2, 100 mM KCl (1 h) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.62 Å / Num. obs: 31257 / % possible obs: 100 % / Redundancy: 19.9 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.028 / Rrim(I) all: 0.127 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 20.3 % / Rmerge(I) obs: 2.337 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2053 / CC1/2: 0.75 / Rpim(I) all: 0.529 / Rrim(I) all: 2.397 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EVB Resolution: 1.9→29.2 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 38.92 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å /
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