[English] 日本語
Yorodumi
- EMDB-3606: Malaria-infected red blood cell section showing a segmented schizont -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3606
TitleMalaria-infected red blood cell section showing a segmented schizont
Map dataResin section tomogram of a malaria infected red blood cell showing a fully segmented schizont.
Sample
  • Cell: Plasmodium falciparum infected human erythrocyte treated with the egress inhibitor Compound 1
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodelectron tomography / negative staining
AuthorsHale VL / Saibil HR
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Parasitophorous vacuole poration precedes its rupture and rapid host erythrocyte cytoskeleton collapse in egress.
Authors: Victoria L Hale / Jean M Watermeyer / Fiona Hackett / Gema Vizcay-Barrena / Christiaan van Ooij / James A Thomas / Matthew C Spink / Maria Harkiolaki / Elizabeth Duke / Roland A Fleck / ...Authors: Victoria L Hale / Jean M Watermeyer / Fiona Hackett / Gema Vizcay-Barrena / Christiaan van Ooij / James A Thomas / Matthew C Spink / Maria Harkiolaki / Elizabeth Duke / Roland A Fleck / Michael J Blackman / Helen R Saibil /
Abstract: In the asexual blood stages of malarial infection, merozoites invade erythrocytes and replicate within a parasitophorous vacuole to form daughter cells that eventually exit (egress) by sequential ...In the asexual blood stages of malarial infection, merozoites invade erythrocytes and replicate within a parasitophorous vacuole to form daughter cells that eventually exit (egress) by sequential rupture of the vacuole and erythrocyte membranes. The current model is that PKG, a malarial cGMP-dependent protein kinase, triggers egress, activating malarial proteases and other effectors. Using selective inhibitors of either PKG or cysteine proteases to separately inhibit the sequential steps in membrane perforation, combined with video microscopy, electron tomography, electron energy loss spectroscopy, and soft X-ray tomography of mature intracellular parasites, we resolve intermediate steps in egress. We show that the parasitophorous vacuole membrane (PVM) is permeabilized 10-30 min before its PKG-triggered breakdown into multilayered vesicles. Just before PVM breakdown, the host red cell undergoes an abrupt, dramatic shape change due to the sudden breakdown of the erythrocyte cytoskeleton, before permeabilization and eventual rupture of the erythrocyte membrane to release the parasites. In contrast to the previous view of PKG-triggered initiation of egress and a gradual dismantling of the host erythrocyte cytoskeleton over the course of schizont development, our findings identify an initial step in egress and show that host cell cytoskeleton breakdown is restricted to a narrow time window within the final stages of egress.
History
DepositionFeb 28, 2017-
Header (metadata) releaseMar 22, 2017-
Map releaseMar 22, 2017-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3606.png

Downloads & links

-
Map

FileDownload / File: emd_3606.map.gz / Format: CCP4 / Size: 71.3 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationResin section tomogram of a malaria infected red blood cell showing a fully segmented schizont.
Voxel sizeX=Y=Z: 16.25796 Å
Density
Minimum - Maximum-128. - 127.
Average (Standard dev.)93.034180000000006 (±6.297862)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-45-5340
Dimensions96595781
Spacing95796581
CellA: 15558.867 Å / B: 15688.929 Å / C: 1316.8947 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z16.25795924764916.25795751295316.257962962963
M x/y/z95796581
origin x/y/z0.0000.0000.000
length x/y/z15558.86715688.9291316.895
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-53-4540
NC/NR/NS95796581
D min/max/mean-128.000127.00093.034

-
Supplemental data

-
Sample components

-
Entire : Plasmodium falciparum infected human erythrocyte treated with the...

EntireName: Plasmodium falciparum infected human erythrocyte treated with the egress inhibitor Compound 1
Components
  • Cell: Plasmodium falciparum infected human erythrocyte treated with the egress inhibitor Compound 1

-
Supramolecule #1: Plasmodium falciparum infected human erythrocyte treated with the...

SupramoleculeName: Plasmodium falciparum infected human erythrocyte treated with the egress inhibitor Compound 1
type: cell / ID: 1 / Parent: 0
Details: High pressure frozen and freeze-substituted cell section
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7 / Details: RPMI medium
StainingType: NEGATIVE / Material: Uranyl Acetate
Sugar embeddingMaterial: HM20 / Details: Freeze substitution
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
High pressure freezingInstrument: OTHER
Details: The value given for _emd_high_pressure_freezing.instrument is Baltech HPM010. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION ...Details: The value given for _emd_high_pressure_freezing.instrument is Baltech HPM010. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM HPM100', 'BAL-TEC HPM 010']) so OTHER is written into the XML file.
SectioningUltramicrotomy - Instrument: Leica EM UC7 / Ultramicrotomy - Temperature: 293 K / Ultramicrotomy - Final thickness: 100
Fiducial markerManufacturer: Electron Microscopy Sciences / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: OTHER

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 127

+
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