[English] 日本語
Yorodumi
- EMDB-29754: Cryptosporidium parvum sporozoite apical end -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29754
TitleCryptosporidium parvum sporozoite apical end
Map dataCryptosporidium parvum apical end
Sample
  • Cell: Cryptosporidium parvum sporozoite apical complex
KeywordsConoid / Parasite / preconoidal rings / CELL INVASION
Biological speciesCryptosporidium parvum Iowa (eukaryote)
Methodelectron tomography / cryo EM
AuthorsMartinez M / Chang Y-W / Mageswaran SK
Funding support United States, 1 items
OrganizationGrant numberCountry
David and Lucile Packard Foundation United States
CitationJournal: Nat Commun / Year: 2023
Title: Origin and arrangement of actin filaments for gliding motility in apicomplexan parasites revealed by cryo-electron tomography.
Authors: Matthew Martinez / Shrawan Kumar Mageswaran / Amandine Guérin / William David Chen / Cameron Parker Thompson / Sabine Chavin / Dominique Soldati-Favre / Boris Striepen / Yi-Wei Chang /
Abstract: The phylum Apicomplexa comprises important eukaryotic parasites that invade host tissues and cells using a unique mechanism of gliding motility. Gliding is powered by actomyosin motors that ...The phylum Apicomplexa comprises important eukaryotic parasites that invade host tissues and cells using a unique mechanism of gliding motility. Gliding is powered by actomyosin motors that translocate host-attached surface adhesins along the parasite cell body. Actin filaments (F-actin) generated by Formin1 play a central role in this critical parasitic activity. However, their subcellular origin, path and ultrastructural arrangement are poorly understood. Here we used cryo-electron tomography to image motile Cryptosporidium parvum sporozoites and reveal the cellular architecture of F-actin at nanometer-scale resolution. We demonstrate that F-actin nucleates at the apically positioned preconoidal rings and is channeled into the pellicular space between the parasite plasma membrane and the inner membrane complex in a conoid extrusion-dependent manner. Within the pellicular space, filaments on the inner membrane complex surface appear to guide the apico-basal flux of F-actin. F-actin concordantly accumulates at the basal end of the parasite. Finally, analyzing a Formin1-depleted Toxoplasma gondii mutant pinpoints the upper preconoidal ring as the conserved nucleation hub for F-actin in Cryptosporidium and Toxoplasma. Together, we provide an ultrastructural model for the life cycle of F-actin for apicomplexan gliding motility.
History
DepositionFeb 13, 2023-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateSep 13, 2023-
Current statusSep 13, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29754.png

Downloads & links

-
Map

FileDownload / File: emd_29754.map.gz / Format: CCP4 / Size: 842.9 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationCryptosporidium parvum apical end
Voxel sizeX=Y=Z: 10.6 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)28.004677000000001 (±4.786081)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin209-209300
Dimensions14401023600
Spacing10231440600
CellA: 10843.801 Å / B: 15264.001 Å / C: 6360.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Cryptosporidium parvum sporozoite apical complex

EntireName: Cryptosporidium parvum sporozoite apical complex
Components
  • Cell: Cryptosporidium parvum sporozoite apical complex

-
Supramolecule #1: Cryptosporidium parvum sporozoite apical complex

SupramoleculeName: Cryptosporidium parvum sporozoite apical complex / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Cryptosporidium parvum Iowa (eukaryote)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 310 K / Instrument: LEICA EM GP / Details: Front blot for 4 seconds before plunging.
DetailsExcysted sporozoites from isolated oocysts
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Ted Pella, Inc / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 33000
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
SoftwareName: SerialEM (ver. 3.8)
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 61 / Average exposure time: 0.4 sec. / Average electron dose: 2.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.11.5) / Number images used: 61
DetailsRaw frames were gain normalized in serialEM and motion corrected using the alignframes command in IMOD

+
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://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