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Yorodumi- EMDB-9208: Plasmodium falciparum 80S ribosome bound to the anti-protozoan dr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9208 | |||||||||
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Title | Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine using (Topaz t-2) - (published) picks (EMPIAR-10028 reprocessing) | |||||||||
Map data | Cryosparc v0 with (Topaz t-4) - (published) picks sharpened | |||||||||
Sample |
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Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.12 Å | |||||||||
Authors | Bepler T / Morin A / Brasch J / Shapiro L / Noble AJ / Berger B | |||||||||
Citation | Journal: Elife / Year: 2014 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9208.map.gz | 230 MB | EMDB map data format | |
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Header (meta data) | emd-9208-v30.xml emd-9208.xml | 19 KB 19 KB | Display Display | EMDB header |
Images | emd_9208.png | 92.3 KB | ||
Masks | emd_9208_msk_1.map | 244.1 MB | Mask map | |
Others | emd_9208_additional.map.gz emd_9208_half_map_1.map.gz emd_9208_half_map_2.map.gz | 121.6 MB 226.3 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9208 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9208 | HTTPS FTP |
-Validation report
Summary document | emd_9208_validation.pdf.gz | 77.7 KB | Display | EMDB validaton report |
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Full document | emd_9208_full_validation.pdf.gz | 76.8 KB | Display | |
Data in XML | emd_9208_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9208 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9208 | HTTPS FTP |
-Related structure data
Related structure data | 9194C 9201C 9202C 9206C 9207C 9209C 9210C 9211C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9208.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryosparc v0 with (Topaz t-4) - (published) picks sharpened | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | emd_9208_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Cryosparc v0 with (Topaz t-4) - (published) picks unsharpened
File | emd_9208_additional.map | ||||||||||||
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Annotation | Cryosparc v0 with (Topaz t-4) - (published) picks unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryosparc v0 with (Topaz t-4) - (published) picks half map
File | emd_9208_half_map_1.map | ||||||||||||
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Annotation | Cryosparc v0 with (Topaz t-4) - (published) picks half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryosparc v0 with (Topaz t-4) - (published) picks half map
File | emd_9208_half_map_2.map | ||||||||||||
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Annotation | Cryosparc v0 with (Topaz t-4) - (published) picks half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-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: (Topaz t-2) - (published) picks |
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Source (natural) | Organism: Plasmodium falciparum (malaria parasite P. falciparum) |
Recombinant expression | Organism: Plasmodium falciparum (malaria parasite P. falciparum) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 | Support film - Material: CARBON / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV / Details: Blot 2.5 seconds before plunging.. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 78000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |