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- EMDB-55336: electron tomograms of epon embedded P. falciparum stage V gametoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-55336
Titleelectron tomograms of epon embedded P. falciparum stage V gametocytes with PfMIC19/PfMIC60 double knockout
Map databackprojection tomogram 03
Sample
  • Cell: P. falciparum stage V gametocyte (PfMIC19/PfMIC60 double KO)
Keywordsmitochondrion / cristae / plasmodium / MICOS / MIC60 / STRUCTURAL PROTEIN
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodelectron tomography / negative staining
AuthorsBregy I / Tassan-Lugrezin S / Lopez Orra J / 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
DepositionOct 9, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55336.png

Downloads & links

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Map

FileDownload / File: emd_55336.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotationbackprojection tomogram 03
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
15.2 Å/pix.
x 141 pix.
= 2143.2 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)

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Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 15.2 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-8414.0 - 5000.0
Average (Standard dev.)367.133420000000001 (±228.348919999999993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-65
Dimensions20482048141
Spacing20482048141
CellA: 31129.6 Å / B: 31129.6 Å / C: 2143.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: backprojection tomogram 01

Fileemd_55336_additional_1.map
Annotationbackprojection tomogram 01
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Additional map: backprojection tomogram 14

Fileemd_55336_additional_10.map
Annotationbackprojection tomogram 14
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Additional map: backprojection tomogram 11

Fileemd_55336_additional_11.map
Annotationbackprojection tomogram 11
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Additional map: backprojection tomogram 13

Fileemd_55336_additional_12.map
Annotationbackprojection tomogram 13
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Additional map: backprojection tomogram 12

Fileemd_55336_additional_13.map
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Additional map: backprojection tomogram 15

Fileemd_55336_additional_14.map
Annotationbackprojection tomogram 15
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Additional map: backprojection tomogram 02

Fileemd_55336_additional_2.map
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Additional map: backprojection tomogram 06

Fileemd_55336_additional_3.map
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Additional map: backprojection tomogram 05

Fileemd_55336_additional_4.map
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Additional map: backprojection tomogram 07

Fileemd_55336_additional_5.map
Annotationbackprojection tomogram 07
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Additional map: backprojection tomogram 04

Fileemd_55336_additional_6.map
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Additional map: backprojection tomogram 08

Fileemd_55336_additional_7.map
Annotationbackprojection tomogram 08
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Additional map: backprojection tomogram 09

Fileemd_55336_additional_8.map
Annotationbackprojection tomogram 09
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Additional map: backprojection tomogram 10

Fileemd_55336_additional_9.map
Annotationbackprojection tomogram 10
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Sample components

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Entire : P. falciparum stage V gametocyte (PfMIC19/PfMIC60 double KO)

EntireName: P. falciparum stage V gametocyte (PfMIC19/PfMIC60 double KO)
Components
  • Cell: P. falciparum stage V gametocyte (PfMIC19/PfMIC60 double KO)

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Supramolecule #1: P. falciparum stage V gametocyte (PfMIC19/PfMIC60 double KO)

SupramoleculeName: P. falciparum stage V gametocyte (PfMIC19/PfMIC60 double KO)
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 mic19/60-

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Experimental details

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Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 6.9
StainingType: POSITIVE / Material: Osmium tetroxide, uranyl acetate
Sugar embeddingMaterial: epon
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: FORMVAR / Support film - topology: CONTINUOUS
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: 293 K / Ultramicrotomy - Final thickness: 250
Fiducial markerManufacturer: aurion / Diameter: 15 nm

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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

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Image processing

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

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