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- EMDB-9206: Plasmodium falciparum 80S ribosome bound to the anti-protozoan dr... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9206 | |||||||||
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Title | Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine using published picks (EMPIAR-10028 reprocessing) | |||||||||
![]() | Cryosparc v0 with published picks sharpened | |||||||||
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Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Bepler T / Morin A / Brasch J / Shapiro L / Noble AJ / Berger B | |||||||||
![]() | ![]() Title: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine. Authors: Wilson Wong / Xiao-chen Bai / Alan Brown / Israel S Fernandez / Eric Hanssen / Melanie Condron / Yan Hong Tan / Jake Baum / Sjors H W Scheres / ![]() ![]() Abstract: Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as ...Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as potential anti-malarial therapies. Antibiotics that inhibit protein translation are promising candidates for repositioning. We have solved the cryo-EM structure of the cytoplasmic ribosome from the human malaria parasite, Plasmodium falciparum, in complex with emetine at 3.2 Å resolution. Emetine is an anti-protozoan drug used in the treatment of ameobiasis that also displays potent anti-malarial activity. Emetine interacts with the E-site of the ribosomal small subunit and shares a similar binding site with the antibiotic pactamycin, thereby delivering its therapeutic effect by blocking mRNA/tRNA translocation. As the first cryo-EM structure that visualizes an antibiotic bound to any ribosome at atomic resolution, this establishes cryo-EM as a powerful tool for screening and guiding the design of drugs that target parasite translation machinery. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 167.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.1 KB 19.1 KB | Display Display | ![]() |
Images | ![]() | 97.9 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Others | ![]() ![]() ![]() | 88.2 MB 164.9 MB 164.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9194C ![]() 9201C ![]() 9202C ![]() 9207C ![]() 9208C ![]() 9209C ![]() 9210C ![]() 9211C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryosparc v0 with published picks sharpened | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Cryosparc v0 with published picks unsharpened
File | emd_9206_additional.map | ||||||||||||
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Annotation | Cryosparc v0 with published picks unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryosparc v0 with published picks half map
File | emd_9206_half_map_1.map | ||||||||||||
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Annotation | Cryosparc v0 with published picks half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryosparc v0 with published picks half map
File | emd_9206_half_map_2.map | ||||||||||||
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Annotation | Cryosparc v0 with published picks half map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Plasmodium falciparum 80S ribosome bound to the anti-protozoan dr...
Entire | Name: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine |
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Components |
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-Supramolecule #1: Plasmodium falciparum 80S ribosome bound to the anti-protozoan dr...
Supramolecule | Name: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine type: complex / ID: 1 / Parent: 0 / Details: published picks |
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Source (natural) | Organism: ![]() ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.6 mg/mL |
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Buffer | pH: 7.4 Details: 20 mM Hepes pH7.4, 40 mM KCH3COO, 10 mM NH4CH3COO, 10 mM Mg(CH3COO)2 and 5 mM 2-mecaptoethanol |
Grid | Model: Quantifoil R2/2 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Details: home-made continuous carbon film |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV / Details: Blot 2.5 seconds before plunging.. |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2 |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 105247 Details: All initial particles were used in the final reconstruction; ie. no particle filtering or classification was performed. |
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Startup model | Type of model: INSILICO MODEL / In silico model: Cryosparc v0 ab initio |
Initial angle assignment | Type: OTHER / Details: Cryosparc v0 |
Final angle assignment | Type: OTHER / Details: Cryosparc v0 |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - Version: 0 / Number images used: 105247 |
Details | CryoSparc v0 homogeneous 3D refinement. No particle pre-processing. |