+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1125 | |||||||||
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Title | Localization and dynamic behavior of ribosomal protein L30e. | |||||||||
Map data | 80s wheat germ ribosome | |||||||||
Sample |
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Function / homology | Function and homology information small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / ribosome / structural constituent of ribosome / translation / nucleolus / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Triticum sp. (plant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.5 Å | |||||||||
Authors | Halic M | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2005 Title: Localization and dynamic behavior of ribosomal protein L30e. Authors: Mario Halic / Thomas Becker / Joachim Frank / Christian M T Spahn / Roland Beckmann / Abstract: The ribosomal protein L30e is an indispensable component of the eukaryotic 80S ribosome, where it is part of the large (60S) ribosomal subunit. Here, we determined the localization of L30e in the ...The ribosomal protein L30e is an indispensable component of the eukaryotic 80S ribosome, where it is part of the large (60S) ribosomal subunit. Here, we determined the localization of L30e in the cryo-EM map of the 80S wheat germ (wg) ribosome at a resolution of 9.5 A. L30e is part of the interface between large and small subunits, where it dynamically participates in the formation of the two intersubunit bridges eB9 and B4. | |||||||||
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_1125.map.gz | 17.2 MB | EMDB map data format | |
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Header (meta data) | emd-1125-v30.xml emd-1125.xml | 6.5 KB 6.5 KB | Display Display | EMDB header |
Images | 1125.gif | 10.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1125 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1125 | HTTPS FTP |
-Validation report
Summary document | emd_1125_validation.pdf.gz | 328.6 KB | Display | EMDB validaton report |
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Full document | emd_1125_full_validation.pdf.gz | 328.2 KB | Display | |
Data in XML | emd_1125_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1125 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1125 | HTTPS FTP |
-Related structure data
Related structure data | 1yshMC M: atomic model generated by this map 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_1125.map.gz / Format: CCP4 / Size: 40.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 80s wheat germ ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : 80s wheat germ ribosome
Entire | Name: 80s wheat germ ribosome |
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Components |
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-Supramolecule #1000: 80s wheat germ ribosome
Supramolecule | Name: 80s wheat germ ribosome / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: 80s
Supramolecule | Name: 80s / type: complex / ID: 1 / Name.synonym: 80s / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Triticum sp. (plant) / synonym: Bread wheat |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE |
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-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Digitization - Scanner: OTHER / Digitization - Sampling interval: 1.6 µm |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: gg / Specimen holder model: GATAN HELIUM |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider |
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