[English] 日本語
Yorodumi
- EMDB-28140: Toxoplasma gondii apical complex (non-stimulated) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28140
TitleToxoplasma gondii apical complex (non-stimulated)
Map dataToxoplasma gondii apical complex (non-stimulated)
Sample
  • Organelle or cellular component: The apical complex of Toxoplasma gondii (non-stimulated)
KeywordsToxoplasma gondii / apical complex / non-stimulated / CELL INVASION
Biological speciesToxoplasma gondii (eukaryote)
Methodelectron tomography / cryo EM
AuthorsSegev-Zarko L / Sun SY / Chiu W / Boothroyd JC
Funding support United States, 2 items
OrganizationGrant numberCountry
Other private United States
Other government
CitationJournal: PNAS Nexus / Year: 2022
Title: Cryo-electron tomography with mixed-scale dense neural networks reveals key steps in deployment of invasion machinery.
Authors: Li-Av Segev-Zarko / Peter D Dahlberg / Stella Y Sun / Daniël M Pelt / Chi Yong Kim / Elizabeth S Egan / James A Sethian / Wah Chiu / John C Boothroyd /
Abstract: Host cell invasion by intracellular, eukaryotic parasites within the phylum Apicomplexa is a remarkable and active process involving the coordinated action of apical organelles and other structures. ...Host cell invasion by intracellular, eukaryotic parasites within the phylum Apicomplexa is a remarkable and active process involving the coordinated action of apical organelles and other structures. To date, capturing how these structures interact during invasion has been difficult to observe in detail. Here, we used cryogenic electron tomography to image the apical complex of tachyzoites under conditions that mimic resting parasites and those primed to invade through stimulation with calcium ionophore. Through the application of mixed-scale dense networks for image processing, we developed a highly efficient pipeline for annotation of tomograms, enabling us to identify and extract densities of relevant subcellular organelles and accurately analyze features in 3-D. The results reveal a dramatic change in the shape of the anteriorly located apical vesicle upon its apparent fusion with a rhoptry that occurs only in the stimulated parasites. We also present information indicating that this vesicle originates from the vesicles that parallel the intraconoidal microtubules and that the latter two structures are linked by a novel tether. We show that a rosette structure previously proposed to be involved in rhoptry secretion is associated with apical vesicles beyond just the most anterior one. This result, suggesting multiple vesicles are primed to enable rhoptry secretion, may shed light on the mechanisms employs to enable repeated invasion attempts. Using the same approach, we examine merozoites and show that they too possess an apical vesicle just beneath a rosette, demonstrating evolutionary conservation of this overall subcellular organization.
History
DepositionSep 13, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28140.png

Downloads & links

-
Map

FileDownload / File: emd_28140.map.gz / Format: CCP4 / Size: 355.1 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationToxoplasma gondii apical complex (non-stimulated)
Voxel sizeX=Y=Z: 13.84 Å
Density
Minimum - Maximum-584.0 - 482.0
Average (Standard dev.)1.8708776 (±18.162770999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00105
Dimensions928960209
Spacing960928209
CellA: 13286.4 Å / B: 12843.5205 Å / C: 2892.56 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : The apical complex of Toxoplasma gondii (non-stimulated)

EntireName: The apical complex of Toxoplasma gondii (non-stimulated)
Components
  • Organelle or cellular component: The apical complex of Toxoplasma gondii (non-stimulated)

-
Supramolecule #1: The apical complex of Toxoplasma gondii (non-stimulated)

SupramoleculeName: The apical complex of Toxoplasma gondii (non-stimulated)
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Toxoplasma gondii (eukaryote) / Strain: RH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.2 / Component - Concentration: 1.0 x / Component - Name: Endo buffer
Details: 45 mM potassium sulfate, 106 mM sucrose, 10 mM magnesium sulfate, 20 mM Tris buffer pH 7.2, 5 mM glucose and 0.35% bovine serum albumin
GridModel: EMS Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 297 K / Instrument: LEICA EM GP
DetailsTachyzoites were released from heavily infected monolayers of HFFs by mechanical disruption of the monolayers using disposable scrapers and passage through a 25-gauge syringe into HPEB
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: EMS / Diameter: 10 nm

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 26000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 61

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more