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- EMDB-28141: 3D reconstruction of the apical complex of Plasmodium falciparum ... -

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Entry
Database: EMDB / ID: EMD-28141
Title3D reconstruction of the apical complex of Plasmodium falciparum (3D7) free merozoite
Map data3D reconstruction of the apical complex of Plasmodium falciparum (3D7) free merozoite (top view)
Sample
  • Cell: Plasmodium falciparum (3D7) free merozoite
KeywordsFree merozoite / Plasmodium falciparum / top view / CELL INVASION
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodelectron tomography / cryo EM
AuthorsSegev-Zarko L / Sun SY / Kim CY
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD021600 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
Other privateFI-582-2018
Other privateStanford Maternal and Child Health Research Institute
Other privateStanford School of Medicine Deans Postdoctoral Fellowship
Other privateCZI Biohub Intercampus Team Award
Other privateStanford ChEM-H Seed Grant
CitationJournal: mBio / Year: 2024
Title: Cryogenic electron tomography reveals novel structures in the apical complex of .
Authors: Stella Y Sun / Li-Av Segev-Zarko / Grigore D Pintilie / Chi Yong Kim / Sophia R Staggers / Michael F Schmid / Elizabeth S Egan / Wah Chiu / John C Boothroyd /
Abstract: Intracellular infectious agents, like the malaria parasite, , face the daunting challenge of how to invade a host cell. This problem may be even harder when the host cell in question is the ...Intracellular infectious agents, like the malaria parasite, , face the daunting challenge of how to invade a host cell. This problem may be even harder when the host cell in question is the enucleated red blood cell, which lacks the host machinery co-opted by many pathogens for internalization. Evolution has provided and related single-celled parasites within the phylum Apicomplexa with a collection of organelles at their apical end that mediate invasion. This apical complex includes at least two sets of secretory organelles, micronemes and rhoptries, and several structural features like apical rings and a putative pore through which proteins may be introduced into the host cell during invasion. We perform cryogenic electron tomography (cryo-ET) equipped with Volta Phase Plate on isolated and vitrified merozoites to visualize the apical machinery. Through tomographic reconstruction of cellular compartments, we see new details of known structures like the rhoptry tip interacting directly with a rosette resembling the recently described rhoptry secretory apparatus (RSA) or with an apical vesicle docked beneath the RSA. Subtomogram averaging reveals that the apical rings have a fixed number of repeating units, each of which is similar in overall size and shape to the units in the apical rings of tachyzoites of . Comparison of these polar rings in and parasites also reveals them to have a structurally conserved assembly pattern. These results provide new insight into the essential and structurally conserved features of this remarkable machinery used by apicomplexan parasites to invade their respective host cells.
IMPORTANCE: Malaria is an infectious disease caused by parasites of the genus and is a leading cause of morbidity and mortality globally. Upon infection, parasites invade and replicate in red blood ...IMPORTANCE: Malaria is an infectious disease caused by parasites of the genus and is a leading cause of morbidity and mortality globally. Upon infection, parasites invade and replicate in red blood cells, where they are largely protected from the immune system. To enter host cells, the parasites employ a specialized apparatus at their anterior end. In this study, advanced imaging techniques like cryogenic electron tomography (cryo-ET) and Volta Phase Plate enable unprecedented visualization of whole merozoites, revealing previously unknown structural details of their invasion machinery. Key findings include new insights into the structural conservation of apical rings shared between and its apicomplexan cousin, . These discoveries shed light on the essential and conserved elements of the invasion machinery used by these pathogens. Moreover, the research provides a foundation for understanding the molecular mechanisms underlying parasite-host interactions, potentially informing strategies for combating diseases caused by apicomplexan parasites.
History
DepositionSep 13, 2022-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28141.png

Downloads & links

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Map

FileDownload / File: emd_28141.map.gz / Format: CCP4 / Size: 747.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of the apical complex of Plasmodium falciparum (3D7) free merozoite (top view)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.17 Å/pix.
x 220 pix.
= 3117.4 Å		14.17 Å/pix.
x 960 pix.
= 13603.2 Å		14.17 Å/pix.
x 928 pix.
= 13149.76 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: 14.17 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-16.582203 - 10.075288
Average (Standard dev.)0.088448085 (±0.9026287)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin16-16110
Dimensions960928220
Spacing928960220
CellA: 13149.76 Å / B: 13603.2 Å / C: 3117.4 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 (3D7) free merozoite

EntireName: Plasmodium falciparum (3D7) free merozoite
Components
  • Cell: Plasmodium falciparum (3D7) free merozoite

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Supramolecule #1: Plasmodium falciparum (3D7) free merozoite

SupramoleculeName: Plasmodium falciparum (3D7) free merozoite / 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: 7.4 / Component - Concentration: 1.0 x / Component - Name: PBS
GridModel: Homemade / Material: COPPER / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: LEICA EM GP / Details: 5x10^6-5x10^7 cells/ml.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: EMS / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS TALOS
Electron beamAcceleration voltage: 200 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: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 39000
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.7 e/Å2

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 52

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