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- EMDB-50857: Hemozoin crystals within Plasmodium falciparum digestive vacuole -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50857
TitleHemozoin crystals within Plasmodium falciparum digestive vacuole
Map dataTomographic reconstruction of tilt series showing digestive vacuole of Plasmodium cell containing abundant hemozoin crystals.
Sample
  • Cell: Plasmodium falciparum digestive vacuole
Keywordsmalaria / heme / food vacuole / crystal / CELL INVASION
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodelectron tomography / cryo EM
AuthorsMullick D / Elbaum M
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Hemozoin crystals within Plasmodium falciparum digestive vacuole
Authors: Mullick D / Elbaum M
History
DepositionJul 2, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50857.png

Downloads & links

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Map

FileDownload / File: emd_50857.map.gz / Format: CCP4 / Size: 3.9 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationTomographic reconstruction of tilt series showing digestive vacuole of Plasmodium cell containing abundant hemozoin crystals.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
19.53 Å/pix.
x 500 pix.
= 9765. Å		19.53 Å/pix.
x 2048 pix.
= 39997.441 Å		19.53 Å/pix.
x 2048 pix.
= 39997.441 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: 19.53 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-32768.0 - 32767.0
Average (Standard dev.)39.578049999999998 (±1169.480499999999893)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-350
Dimensions20482048500
Spacing20482048500
CellA: 39997.44 Å / B: 39997.44 Å / C: 9765.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Plasmodium falciparum digestive vacuole

EntireName: Plasmodium falciparum digestive vacuole
Components
  • Cell: Plasmodium falciparum digestive vacuole

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Supramolecule #1: Plasmodium falciparum digestive vacuole

SupramoleculeName: Plasmodium falciparum digestive vacuole / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.3
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 25 K / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: home-made / Diameter: 15 nm

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number real images: 61 / Average exposure time: 50.0 sec. / Average electron dose: 3.875 e/Å2
Details: total exposure in the tomogram 240 electrons/Angstrom squared.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Detailsbuilt-in STEM detector
Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 61
CTF correctionType: NONE

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