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- EMDB-61260: High-resolution cryo-EM structure of the Plasmodium falciparum 80... -

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Basic information

Entry
Database: EMDB / ID: EMD-61260
TitleHigh-resolution cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to E-tRNA (Small Ribosomal Subunit Body)
Map data
Sample
  • Complex: Plasmodium falciparum cytoplasmic ribosomes
Keywordscryo-EM / Plasmodium falciparum / RIBOSOME
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsYan XF / Gao YG
Funding support Singapore, 2 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE-T2EP30122-0019 Singapore
Ministry of Education (MoE, Singapore)RG108/20 Singapore
CitationJournal: Structure / Year: 2025
Title: Antimalarial drug artemisinin stabilizes PfRACK1 binding to the ribosome.
Authors: Ka Diam Go / Xin-Fu Yan / Grennady Wirjanata / Rya Ero / Samuel Pazicky / Jerzy Dziekan / Seth Tjia / Julien Lescar / Zbynek Bozdech / Yong-Gui Gao /
Abstract: Artemisinin and its derivatives represent the core agents in artemisinin combination therapies that are the current frontline treatment for P. falciparum and P. vivax malaria infections. Artemisinins ...Artemisinin and its derivatives represent the core agents in artemisinin combination therapies that are the current frontline treatment for P. falciparum and P. vivax malaria infections. Artemisinins are known to bind a wide array of proteins that disrupt the parasite's cellular physiology. Here, we show that artemisinins' cytotoxic activity involves structural alteration of key P. falciparum macromolecular complexes, including the ribosome, proteasome, and T-complex. The structural analysis revealed that, following artemisinin treatment, a larger population of Pf80S ribosomes binds PfRACK1. Unlike in most eukaryotes, PfRACK1 does not interact with the C-terminal tail of the r-protein uS3 that in Plasmodium is truncated. This likely suggests an evolved role of uS3 in facilitating RACK1-mediated translational regulation, which would potentially benefit the parasite under certain conditions. Stabilization of RACK1 ribosome interaction likely contributes to artemisinins' mode of action.
History
DepositionAug 22, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61260.png

Downloads & links

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Map

FileDownload / File: emd_61260.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 480 pix.
= 465.6 Å		0.97 Å/pix.
x 480 pix.
= 465.6 Å		0.97 Å/pix.
x 480 pix.
= 465.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.0062186928 - 0.015240633
Average (Standard dev.)-0.000022321527 (±0.00039221384)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 465.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61260_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_61260_half_map_1.map
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Half map: #2

Fileemd_61260_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Plasmodium falciparum cytoplasmic ribosomes

EntireName: Plasmodium falciparum cytoplasmic ribosomes
Components
  • Complex: Plasmodium falciparum cytoplasmic ribosomes

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Supramolecule #1: Plasmodium falciparum cytoplasmic ribosomes

SupramoleculeName: Plasmodium falciparum cytoplasmic ribosomes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#79
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85400
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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