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- EMDB-32630: Structure and dynamics of Odinarchaeota tubulin and the implicati... -

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Entry
Database: EMDB / ID: EMD-32630
TitleStructure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution
Map dataReconstruction of tubes of OdinTubulin sampled from Yellowstone Lower Culex Basin hot spring polymerized at 37 degrees Celsius
Sample
  • Complex: Tubulin homolog from Candidatus Odinarchaeota archaeon
    • Other: OdinTubulin
KeywordsEukaryotic tubulin homolog / STRUCTURAL PROTEIN
Biological speciesCandidatus Odinarchaeota archaeon LCB_4 (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 28.82 Å
AuthorsAkil C / Ali S / Tran LT
Funding support3 items
OrganizationGrant numberCountry
Japan Science and TechnologyJST CREST-JPMJCR19S5
Japan Society for the Promotion of Science (JSPS)JP20H00476
Other governmentMoore-Simons Project on the Origin of the Eukaryotic Cell-GBMF9743
CitationJournal: 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
DepositionJan 18, 2022-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32630.png

Downloads & links

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Map

FileDownload / File: emd_32630.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of tubes of OdinTubulin sampled from Yellowstone Lower Culex Basin hot spring polymerized at 37 degrees Celsius
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.25 Å/pix.
x 200 pix.
= 1450. Å		7.25 Å/pix.
x 200 pix.
= 1450. Å		7.25 Å/pix.
x 200 pix.
= 1450. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.07558913 - 0.16570498
Average (Standard dev.)0.00047502512 (±0.007304681)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 1450.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tubulin homolog from Candidatus Odinarchaeota archaeon

EntireName: Tubulin homolog from Candidatus Odinarchaeota archaeon
Components
  • Complex: Tubulin homolog from Candidatus Odinarchaeota archaeon
    • Other: OdinTubulin

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Supramolecule #1: Tubulin homolog from Candidatus Odinarchaeota archaeon

SupramoleculeName: 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.
Source (natural)Organism: Candidatus Odinarchaeota archaeon LCB_4 (archaea)
Molecular weightTheoretical: 47.6 kDa/nm

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Macromolecule #1: OdinTubulin

MacromoleculeName: OdinTubulin / type: other / ID: 1
Details: Candidatus Odinarchaeota archaeon LCB_4 (Odin) metagenome-assembled genome
Classification: other
Source (natural)Organism: Candidatus Odinarchaeota archaeon LCB_4 (archaea)
SequenceString: 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 expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration6.8 mg/mL
BufferpH: 6.9
Component:
ConcentrationFormulaName
100.0 mMPIPESPIPES
0.5 mMMgSO4Magnesium suphate
0.5 mMEGTAEGTA
10.0 % (v/v)GlycerolGlycerol

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
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 1217 / Average exposure time: 2.42 sec. / Average electron dose: 40.05 e/Å2
Details: 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsImages were recorded using a Falcon III detector (FEI)
Final reconstructionNumber classes used: 3
Applied symmetry - Helical parameters - Δz: 29.05 Å
Applied symmetry - Helical parameters - Δ&Phi: -102.853 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 28.82 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.11)
Software - details: Final 3D and postprocessing were performed in RELION3.11
Number images used: 7368
Segment selectionNumber selected: 126847 / Software - Name: EMAN2 (ver. 2.2)
Software - details: Tubes were selected using EMAN2 e2helixboxer.py.
Details: Tubules were picked manually using EMAN2 e2helixboxer and extracted in RELION3.11 with a binning box size of 250 x 250 pixels
Startup modelType of model: OTHER
Details: Initial model was obtained reconstruction OdinTubulin from initial cryoEM screening samples
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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