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- EMDB-66190: The in situ structure of adjacent conoid fibers from Toxoplasma g... -

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Basic information

Entry
Database: EMDB / ID: EMD-66190
TitleThe in situ structure of adjacent conoid fibers from Toxoplasma gondii tachyzoite
Map data
Sample
  • Cell: Conoid fiber of mature Toxoplasma gondii tachyzoite
KeywordsToxoplasma gondii / conoid / STRUCTURAL PROTEIN
Biological speciesToxoplasma gondii (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 33.4 Å
AuthorsLi Z / Du W / Yang J / Lai D / Lun Z / Guo Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
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
DepositionSep 12, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66190.png

Downloads & links

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Map

FileDownload / File: emd_66190.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
3.33 Å/pix.
x 336 pix.
= 1118.208 Å		3.33 Å/pix.
x 336 pix.
= 1118.208 Å		3.33 Å/pix.
x 336 pix.
= 1118.208 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.328 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00347
Minimum - Maximum-0.003188174 - 0.009581139
Average (Standard dev.)0.00029421167 (±0.001481512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 1118.208 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66190_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_66190_half_map_2.map
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Histogram (log scale)

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Sample components

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Entire : Conoid fiber of mature Toxoplasma gondii tachyzoite

EntireName: Conoid fiber of mature Toxoplasma gondii tachyzoite
Components
  • Cell: Conoid fiber of mature Toxoplasma gondii tachyzoite

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Supramolecule #1: Conoid fiber of mature Toxoplasma gondii tachyzoite

SupramoleculeName: Conoid fiber of mature Toxoplasma gondii tachyzoite / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Toxoplasma gondii (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TITAN THEMIS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 33.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp / Number subtomograms used: 1080
ExtractionNumber tomograms: 10 / Number images used: 1080 / Software - Name: RELION
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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