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

2023-12-13 REL PDBj PDBj PDBj 2022-01-18 2022-04-06 2022-04-06 2023-12-13 Japan Science and Technology JST CREST-JPMJCR19S5 Japan Society for the Promotion of Science (JSPS) JP20H00476 Other government Moore-Simons Project on the Origin of the Eukaryotic Cell-GBMF9743 Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution Akil C Ali S Tran LT Eukaryotic tubulin homolog, STRUCTURAL PROTEIN Akil C Ali S Tran LT Gaillard J Li W Hayashida K Hirose M Kato T Oshima A Fujishima K Blanchoin L Narita A Robinson RC Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution. Sci Adv US 8 eabm2225 eabm2225 2022 35333570 doi:10.1126/sciadv.abm2225 2375-2548 Tubulin homolog from Candidatus Odinarchaeota archaeon Tubulin homolog from Candidatus Odinarchaeota archaeon 0 1

OdinTubulin was sampled from Candidatus Odinarchaeota archaeon LCB_4 MAG whose habitat is Yellowstone Lower Culex Basin hot spring.

Candidatus Odinarchaeota archaeon LCB_4 47.6 OdinTubulin Candidatus Odinarchaeota archaeon LCB_4

Candidatus Odinarchaeota archaeon LCB_4 (Odin) metagenome-assembled genome

PMPGREILVLHVGQGGNQIGYNFWKTICEEHNIDIRSNQRKSVEEDKVDYKSVFLVEAPDGFHPRALFIDLEPLAVEFLVKEMKLGSFFSEDLMVLSYSGAHNVWSIGYQTGKKLIPVILEKIRDTMPETLQGFLIIHTLGGGTGSGFGSLLTETLKKEFPGKGVLNFSVLPSEVNDVTLAPYNTVLSLNHLSRFSDLVVLFDNTALIRIVKDQLNYPVIKQFSDLNFLIGRVMASITASLRFPGPLNMDLMEMAHNLVALPETKFIIPSVAPLTKEESEMSTELDLVERCFDPTHYMVNCSGQGKTISSVLMFRGNIAIENAFSIMTDIKSNVAFAPGVHPDLGLKYGICESAPVDFDKEVTLLSNNTIISEVFNRVLERFDSLFNRDWYTSHYVNAGTSKSNLKEARDNFDRIIKIYKEIEGSQ MDVT00000000.1 other Escherichia coli helical filament 6.8 6.9 100.0 PIPES PIPES 0.5 MgSO4 Magnesium suphate 0.5 EGTA EGTA 10.0 Glycerol Glycerol

100 mM PIPES, pH 6.9, 0.5 mM EGTA, 0.5 mM MgSO4, 10% (v/v) glycerol and polymerized with 2 mM GTP

Quantifoil R2/2 MOLYBDENUM 200 CARBON HOLEY GLOW DISCHARGE 40 AIR

High vacuum

ETHANE 90 298 LEICA EM GP FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.0 2.6 47000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) COUNTING 2 1217 2.42 40.05

Images were recorded using a Falcon3 detector (FEI) at a pixel size of 1.45 angstrom per pixel and a frame rate of 60 frames/individual images

Images were recorded using a Falcon III detector (FEI)

3 29.05 -102.853 C1 BACK PROJECTION 28.82 FSC 0.5 CUT-OFF RELION 3.11 Final 3D and postprocessing were performed in RELION3.11 7368 126847 EMAN2 2.2 Tubes were selected using EMAN2 e2helixboxer.py.

Tubules were picked manually using EMAN2 e2helixboxer and extracted in RELION3.11 with a binning box size of 250 x 250 pixels

Initial model was obtained reconstruction OdinTubulin from initial cryoEM screening samples

NOT APPLICABLE emd_32630.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 1450.0 1450.0 1450.0 90.0 90.0 90.0 X Y Z -0.07558913 0.16570498 0.00047502512 0.007304681 7.25 7.25 7.25 0.038 AUTHOR ::::EMDATABANK.org::::EMD-32630:::: Reconstruction of tubes of OdinTubulin sampled from Yellowstone Lower Culex Basin hot spring polymerized at 37 degrees Celsius