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- EMDB-32629: Structure and dynamics of Odinarchaeota tubulin and the implicati... -
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Open data
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Basic information
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Title | Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution | ||||||||||||
![]() | Reconstruction of tubes of OdinTubulin polymerized at 80 degrees Celsius | ||||||||||||
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![]() | Eukaryotic tubulin homolog / STRUCTURAL PROTEIN | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 37.17 Å | ||||||||||||
![]() | Akil C / Ali S / Tran LT | ||||||||||||
Funding support | 3 items
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 91.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.9 KB 14.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 21.5 KB | Display | ![]() |
Images | ![]() | 55.1 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7evbC ![]() 7evcC ![]() 7evdC ![]() 7eveC ![]() 7evgC ![]() 7evhC ![]() 7eviC ![]() 7evkC ![]() 7evlC ![]() 7f1aC ![]() 7f1bC C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reconstruction of tubes of OdinTubulin polymerized at 80 degrees Celsius | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.22 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Tubulin homolog from Candidatus Odinarchaeota archaeon
Entire | Name: Tubulin homolog from Candidatus Odinarchaeota archaeon |
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Components |
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-Supramolecule #1: Tubulin homolog from Candidatus Odinarchaeota archaeon
Supramolecule | Name: Tubulin homolog from Candidatus Odinarchaeota archaeon type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: OdinTubulin was sampled from Candidatus Odinarchaeota archaeon LCB_4 MAG whose habitat is Yellowstone Lower Culex Basin hot spring. |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 47.6 kDa/nm |
-Macromolecule #1: OdinTubulin
Macromolecule | Name: OdinTubulin / type: other / ID: 1 Details: Candidatus Odinarchaeota archaeon LCB_4 (Odin) metagenome-assembled genome Classification: other |
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Source (natural) | Organism: ![]() |
Sequence | String: PMPGREILVL HVGQGGNQIG YNFWKTICEE HNIDIRSNQR KSVEEDKVDY KSVFLVEAPD GFHPRALFID LEPLAVEFLV KEMKLGSFFS EDLMVLSYSG AHNVWSIGYQ TGKKLIPVIL EKIRDTMPET LQGFLIIHTL GGGTGSGFGS LLTETLKKEF PGKGVLNFSV ...String: PMPGREILVL HVGQGGNQIG YNFWKTICEE HNIDIRSNQR KSVEEDKVDY KSVFLVEAPD GFHPRALFID LEPLAVEFLV KEMKLGSFFS EDLMVLSYSG AHNVWSIGYQ TGKKLIPVIL EKIRDTMPET LQGFLIIHTL GGGTGSGFGS LLTETLKKEF PGKGVLNFSV LPSEVNDVTL APYNTVLSLN HLSRFSDLVV LFDNTALIRI VKDQLNYPVI KQFSDLNFLI GRVMASITAS LRFPGPLNMD LMEMAHNLVA LPETKFIIPS VAPLTKEESE MSTELDLVER CFDPTHYMVN CSGQGKTISS VLMFRGNIAI ENAFSIMTDI KSNVAFAPGV HPDLGLKYGI CESAPVDFDK EVTLLSNNTI ISEVFNRVLE RFDSLFNRDW YTSHYVNAGT SKSNLKEARD NFDRIIKIYK EIEGSQ GENBANK: GENBANK: MDVT00000000.1 |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 6.8 mg/mL | |||||||||||||||
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Buffer | pH: 6.9 Component:
Details: 100 mM PIPES, pH 6.9, 0.5 mM EGTA, 0.5 mM MgSO4, 10% (v/v) glycerol and polymerized with 2 mM GTP | |||||||||||||||
Grid | Model: Quantifoil R2/2 / Material: MOLYBDENUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Details: High vacuum | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 7600 / Average exposure time: 5.21 sec. / Average electron dose: 50.0 e/Å2 Details: Images were recorded with a K3 summit detector (FEI) in counting mode at a pixel size of 1.11 angstrom per pixel and a frame rate of 58 frames per image |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |