[English] 日本語
![](img/lk-miru.gif)
- PDB-7evi: Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilam... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7evi | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 79% GTP, 21% GDP, Na+, Mg2+ | |||||||||||||||
![]() | Tubulin-like protein | |||||||||||||||
![]() | STRUCTURAL PROTEIN / Asgard / tubulin / GTP / filament | |||||||||||||||
Function / homology | ![]() microtubule-based process / structural constituent of cytoskeleton / microtubule / GTPase activity / GTP binding Similarity search - Function | |||||||||||||||
Biological species | Odinarchaeota archaeon | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Robinson, R.C. / Akil, C. / Tran, L.T. | |||||||||||||||
Funding support | ![]() ![]()
| |||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 205 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 153.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 33.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7evbC ![]() 7evcSC ![]() 7evdC ![]() 7eveC ![]() 7evgC ![]() 7evhC ![]() 7evkC ![]() 7evlC ![]() 7f1aC ![]() 7f1bC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
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.) ![]() Strain: LCB_4 / Gene: cetZ, OdinLCB4_01330 / Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 408 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GTP / |
---|---|
#3: Chemical | ChemComp-GDP / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.81 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 3350, 0.2 M sodium acetate 0.1 M Bis-Tris propane, pH 8.5. Crystals were soaked with 5 mM GTP, 2 mM MgCl2 (1 h) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→27 Å / Num. obs: 55795 / % possible obs: 98.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.026 / Rrim(I) all: 0.064 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.55→1.58 Å / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2129 / CC1/2: 0.936 / Rpim(I) all: 0.149 / Rrim(I) all: 0.289 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7EVC Resolution: 1.55→26.1 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→26.1 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.605 Å
|