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Yorodumi- EMDB-41494: Subtomogram averaged non-rotated 80S ribosome of the malarial 80S... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41494 | ||||||||||||
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Title | Subtomogram averaged non-rotated 80S ribosome of the malarial 80S ribosome in Plasmodium falciparum-infected human erythrocytes | ||||||||||||
Map data | Plasmodium falciparum Rack1 focussed denoised | ||||||||||||
Sample |
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Keywords | ribosome / malaria / cryoET / in situ / Plasmodium falciparum / TRANSLATION | ||||||||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 4.3 Å | ||||||||||||
Authors | Anton L / Cheng W / Zhu X / Ho CM | ||||||||||||
Funding support | United States, Switzerland, France, 3 items
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Citation | Journal: To Be Published Title: Divergent translational landscape reflects adaptation to biased codon usage in malaria parasites Authors: Anton L / Cheng W / Haile M / Cobb DW / Zhu X / Han L / Li E / Nair A / Lee CL / Ho CM | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41494.map.gz | 65.9 MB | EMDB map data format | |
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Header (meta data) | emd-41494-v30.xml emd-41494.xml | 22.7 KB 22.7 KB | Display Display | EMDB header |
Images | emd_41494.png | 46.1 KB | ||
Filedesc metadata | emd-41494.cif.gz | 4.1 KB | ||
Others | emd_41494_half_map_1.map.gz emd_41494_half_map_2.map.gz | 37.7 MB 37.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41494 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41494 | HTTPS FTP |
-Validation report
Summary document | emd_41494_validation.pdf.gz | 851 KB | Display | EMDB validaton report |
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Full document | emd_41494_full_validation.pdf.gz | 850.6 KB | Display | |
Data in XML | emd_41494_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_41494_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41494 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41494 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41494.map.gz / Format: CCP4 / Size: 73.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Plasmodium falciparum Rack1 focussed denoised | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.094 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Plasmodium falciparum Rack1 focussed half map 2
File | emd_41494_half_map_1.map | ||||||||||||
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Annotation | Plasmodium falciparum Rack1 focussed half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Plasmodium falciparum Rack1 focussed half map 1
File | emd_41494_half_map_2.map | ||||||||||||
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Annotation | Plasmodium falciparum Rack1 focussed half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Plasmodium falciparum 80S ribosome consensus structure
Entire | Name: Plasmodium falciparum 80S ribosome consensus structure |
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Components |
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-Supramolecule #1: Plasmodium falciparum 80S ribosome consensus structure
Supramolecule | Name: 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 |
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Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.93 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 63941 |
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Extraction | Number tomograms: 848 / Number images used: 129617 |
Final angle assignment | Type: OTHER |