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- EMDB-35098: Tomogram of daughter buds in mature Toxoplasma gondii tachyzoite -

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Basic information

Entry
Database: EMDB / ID: EMD-35098
TitleTomogram of daughter buds in mature Toxoplasma gondii tachyzoite
Map data
Sample
  • Cell: Daughter buds in tachyzoite
KeywordsToxoplasma / daughter buds / conoid / tachyzoite / CELL INVASION
Biological speciesToxoplasma gondii RH (eukaryote)
Methodelectron tomography / cryo EM
AuthorsLi Z / Guo Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Adv Sci (Weinh) / Year: 2023
Title: Cryo-Electron Tomography of Toxoplasma gondii Indicates That the Conoid Fiber May Be Derived from Microtubules.
Authors: Zhixun Li / Wenjing Du / Jiong Yang / De-Hua Lai / Zhao-Rong Lun / Qiang Guo /
Abstract: Toxoplasma gondii (T. gondii) is the causative agent of toxoplasmosis and can infect numerous warm-blooded animals. An improved understanding of the fine structure of this parasite can help elucidate ...Toxoplasma gondii (T. gondii) is the causative agent of toxoplasmosis and can infect numerous warm-blooded animals. An improved understanding of the fine structure of this parasite can help elucidate its replication mechanism. Previous studies have resolved the ultrastructure of the cytoskeleton using purified samples, which eliminates their cellular context. Here the application of cryo-electron tomography to visualize T. gondii tachyzoites in their native state is reported. The fine structure and cellular distribution of the cytoskeleton are resolved and analyzed at nanometer resolution. Additionally, the tachyzoite structural characteristics are annotated during its endodyogeny for the first time. By comparing the structural features in mature tachyzoites and their daughter buds, it is proposed that the conoid fiber of the Apicomplexa originates from microtubules. This work represents the detailed molecular anatomy of T. gondii, particularly during the budding replication stage of tachyzoite, and provides a reference for further studies of this fascinating organism.
History
DepositionJan 10, 2023-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35098.png

Downloads & links

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Map

FileDownload / File: emd_35098.map.gz / Format: CCP4 / Size: 246.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 26.624 Å
Density
Minimum - Maximum-6.6005325 - 3.02679
Average (Standard dev.)-0.000000000058191 (±0.30327895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720512175
Spacing512720175
CellA: 13631.488 Å / B: 19169.281 Å / C: 4659.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Daughter buds in tachyzoite

EntireName: Daughter buds in tachyzoite
Components
  • Cell: Daughter buds in tachyzoite

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Supramolecule #1: Daughter buds in tachyzoite

SupramoleculeName: Daughter buds in tachyzoite / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Toxoplasma gondii RH (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.5 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 180
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 38

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