+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2661 | |||||||||
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Title | Cryo-EM structure of the Plasmodium falciparum 80S ribosome | |||||||||
Map data | Cryo-EM map of the Plasmodium falciparum 80S ribosome | |||||||||
Sample |
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Keywords | Plasmodium falciparum 80S ribosome / Cryo-EM | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 3.4 Å | |||||||||
Authors | Wong W / Bai XC / Brown A / Fernandez IS / Hanssen E / Condron M / Tan YH / Baum J / Scheres SHW | |||||||||
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_2661.map.gz | 325.7 MB | EMDB map data format | |
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Header (meta data) | emd-2661-v30.xml emd-2661.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | cover_image_EMD2661.png | 322.4 KB | ||
Others | emd_2661_half_map_1.map.gz emd_2661_half_map_2.map.gz | 277.2 MB 277.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2661 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2661 | HTTPS FTP |
-Validation report
Summary document | emd_2661_validation.pdf.gz | 299.4 KB | Display | EMDB validaton report |
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Full document | emd_2661_full_validation.pdf.gz | 298.5 KB | Display | |
Data in XML | emd_2661_validation.xml.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2661 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2661 | HTTPS FTP |
-Related 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_2661.map.gz / Format: CCP4 / Size: 339.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of the Plasmodium falciparum 80S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 2661 half map 1.map
File | emd_2661_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 2661 half map 2.map
File | emd_2661_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Plasmodium falciparum 80S ribosome
Entire | Name: Plasmodium falciparum 80S ribosome |
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Components |
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-Supramolecule #1000: Plasmodium falciparum 80S ribosome
Supramolecule | Name: Plasmodium falciparum 80S ribosome / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 4.2 MDa / Theoretical: 4.2 MDa |
-Supramolecule #1: Plasmodium falciparum 80S ribosome
Supramolecule | Name: Plasmodium falciparum 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Plasmodium falciparum (malaria parasite P. falciparum) |
Molecular weight | Experimental: 4.2 MDa / Theoretical: 4.2 MDa |
-Experimental details
-Structure determination
Method | negative staining, 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 |
Staining | Type: NEGATIVE / Details: Cryo-EM |
Grid | Details: 30 s on glow-discharged holey carbon grids (Quantifoil R2/2), onto which a home-made continuous carbon film |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV / Method: Blot 2.5 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80 K / Max: 90 K / Average: 85 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 78,000 times magnification |
Date | Jan 28, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 1307 / Average electron dose: 20 e/Å2 Details: An in-house built system was used to intercept the videos from the detector at a rate of 17 frames for the 1 s exposures. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 135922 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 78000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION Details: Use a newly developed statistical movie processing approach to compensate for beam-induced movement. Number images used: 72293 |