[English] 日本語
Yorodumi
- EMDB-54915: electron tomograms of epon embedded P. falciparum stage V gametoc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54915
Titleelectron tomograms of epon embedded P. falciparum stage V gametocytes (NF54)
Map dataBackprojection 11
Sample
  • Cell: P. falciparum stage V gametocyte (NF54)
Keywordsmitochondrion / cristae / plasmodium / MICOS / MIC60 / STRUCTURAL PROTEIN
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodelectron tomography / negative staining
AuthorsBregy I / Tassan-Lugrezin S / Kooij TWA / van Niftrik L
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)OCENW.M.21.087 Netherlands
CitationJournal: Elife / Year: 2026
Title: The role of MICOS in organizing mitochondrial cristae in malaria parasites
Authors: Tassan-Lugrezin S / Bregy I / Lopez Orra J / Proellochs NI / van Gemert GJ / Stoter R / Evers F / Kooij TW / van Niftrik L
History
DepositionAug 28, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54915.png

Downloads & links

-
Map

FileDownload / File: emd_54915.map.gz / Format: CCP4 / Size: 520 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationBackprojection 11
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
15.2 Å/pix.
x 130 pix.
= 1976. Å		15.2 Å/pix.
x 2048 pix.
= 31129.6 Å		15.2 Å/pix.
x 2048 pix.
= 31129.6 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 15.2 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)4.376046 (±24.445789999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-62
Dimensions20482048130
Spacing20482048130
CellA: 31129.6 Å / B: 31129.6 Å / C: 1976.0 Å
α=β=γ: 90.0 °

-
Supplemental data

+
Additional map: Backprojection 7

Fileemd_54915_additional_1.map
AnnotationBackprojection 7
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Backprojection 8

Fileemd_54915_additional_10.map
AnnotationBackprojection 8
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Backprojection 11

Fileemd_54915_additional_11.map
AnnotationBackprojection 11
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Backprojection 1

Fileemd_54915_additional_2.map
AnnotationBackprojection 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Backprojection 10

Fileemd_54915_additional_3.map
AnnotationBackprojection 10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Backprojection 5

Fileemd_54915_additional_4.map
AnnotationBackprojection 5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Backprojection 9

Fileemd_54915_additional_5.map
AnnotationBackprojection 9
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Backprojection 4

Fileemd_54915_additional_6.map
AnnotationBackprojection 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Backprojection 6

Fileemd_54915_additional_7.map
AnnotationBackprojection 6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Backprojection 3

Fileemd_54915_additional_8.map
AnnotationBackprojection 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Backprojection 2

Fileemd_54915_additional_9.map
AnnotationBackprojection 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : P. falciparum stage V gametocyte (NF54)

EntireName: P. falciparum stage V gametocyte (NF54)
Components
  • Cell: P. falciparum stage V gametocyte (NF54)

-
Supramolecule #1: P. falciparum stage V gametocyte (NF54)

SupramoleculeName: P. falciparum stage V gametocyte (NF54) / type: cell / ID: 1 / Parent: 0
Details: 250 nm epon section, dual-tilt +/-60 degrees with 1.5 degree increment, 200kV
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Strain: NF54

-
Experimental details

-
Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 6.9
StainingType: POSITIVE / Material: uranyl acetate, osmium tetroxide
Sugar embeddingMaterial: epon
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 200 / Support film - Material: FORMVAR
High pressure freezingInstrument: OTHER
Details: The value given for _em_high_pressure_freezing.instrument is Leica EMPACT. This is not in a list of allowed values {'BAL-TEC HPM 010', 'LEICA EM PACT', 'LEICA EM HPM100', 'LEICA EM PACT2', ...Details: The value given for _em_high_pressure_freezing.instrument is Leica EMPACT. This is not in a list of allowed values {'BAL-TEC HPM 010', 'LEICA EM PACT', 'LEICA EM HPM100', 'LEICA EM PACT2', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER'} so OTHER is written into the XML file.
SectioningUltramicrotomy - Instrument: ultracut E / Ultramicrotomy - Temperature: 294 K / Ultramicrotomy - Final thickness: 250
Fiducial markerManufacturer: Aurion / Diameter: 15 nm

-
Electron microscopy

MicroscopeJEOL 2100
Image recordingFilm or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 0.36 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.1 µm / Nominal defocus min: 0.0 µm

-
Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 81
CTF correctionType: NONE

+
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