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- EMDB-41486: Subtomogram averaged decoding-1 state of the malarial 80S ribosom... -

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Basic information

Entry
Database: EMDB / ID: EMD-41486
TitleSubtomogram averaged decoding-1 state of the malarial 80S ribosome in Plasmodium falciparum-infected human erythrocytes
Map dataDecoding-1 translational intermediate from P. falciparum postprocessed
Sample
  • Complex: Plasmodium falciparum 80S ribosome consensus structure
Keywordsribosome / malaria / cryoET / in situ / Plasmodium falciparum / TRANSLATION
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 6.8 Å
AuthorsAnton L / Cheng W / Zhu X / Ho CM
Funding support United States, Switzerland, France, 3 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP5OD029613 United States
Swiss National Science Foundation Switzerland
Human Frontier Science Program (HFSP) France
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Integrated structural biology of the native malarial translation machinery and its inhibition by an antimalarial drug.
Authors: Leonie Anton / Wenjing Cheng / Meseret T Haile / Jerzy M Dziekan / David W Cobb / Xiyan Zhu / Leyan Han / Emerson Li / Anjali Nair / Carolyn L Lee / Hanyu Wang / Hangjun Ke / Guoan Zhang / ...Authors: Leonie Anton / Wenjing Cheng / Meseret T Haile / Jerzy M Dziekan / David W Cobb / Xiyan Zhu / Leyan Han / Emerson Li / Anjali Nair / Carolyn L Lee / Hanyu Wang / Hangjun Ke / Guoan Zhang / Emma H Doud / Alan F Cowman / Chi-Min Ho /
Abstract: Our understanding of cellular events is hampered by the gap between the resolution at which we can observe events inside cells and our ability to replicate physiological conditions in test tubes. ...Our understanding of cellular events is hampered by the gap between the resolution at which we can observe events inside cells and our ability to replicate physiological conditions in test tubes. Here, we show in Plasmodium falciparum, a non-model organism of high medical importance, that this gap can be bridged by using an integrated structural biology approach to visualize events inside the cell at molecular resolution. We determined eight high-resolution structures of the native malarial ribosome in actively translating states inside P. falciparum-infected human erythrocytes using in situ cryo-electron tomography. Following perturbation with a Plasmodium-specific translation inhibitor, we then observed a decrease in elongation factor-bound ribosomal states and an apparent upregulation of ribosome biogenesis in inhibitor-treated parasites. Our work elucidates new molecular details of the malarial translation elongation cycle and demonstrates direct multiscale visualization of drug-induced phenotypic changes in the structure and localization of individual molecules within the native cellular context.
History
DepositionAug 5, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41486.png

Downloads & links

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Map

FileDownload / File: emd_41486.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDecoding-1 translational intermediate from P. falciparum postprocessed
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.09 Å/pix.
x 240 pix.
= 502.56 Å		2.09 Å/pix.
x 240 pix.
= 502.56 Å		2.09 Å/pix.
x 240 pix.
= 502.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.094 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.266
Minimum - Maximum-0.4509527 - 1.1214232
Average (Standard dev.)0.013714857 (±0.07188349)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 502.56003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Decoding-1 translational intermediate from P. falciparum half map 1

Fileemd_41486_half_map_1.map
AnnotationDecoding-1 translational intermediate from P. falciparum half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Decoding-1 translational intermediate from P. falciparum half map 2

Fileemd_41486_half_map_2.map
AnnotationDecoding-1 translational intermediate from P. falciparum half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Plasmodium falciparum 80S ribosome consensus structure

EntireName: Plasmodium falciparum 80S ribosome consensus structure
Components
  • Complex: Plasmodium falciparum 80S ribosome consensus structure

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Supramolecule #1: Plasmodium falciparum 80S ribosome consensus structure

SupramoleculeName: Plasmodium falciparum 80S ribosome consensus structure
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#79
Details: Subtomogram averaged consensus structure of the malarial 80S ribosome in Plasmodium falciparum-infected human erythrocytes
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.93 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 2.8000000000000003 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 7881
ExtractionNumber tomograms: 848 / Number images used: 129617
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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