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Yorodumi- EMDB-5805: Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-F... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5805 | |||||||||
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Title | Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-FMRP Complex map) | |||||||||
Map data | Cryo-EM reconstruction of Drosophila 80S ribosome | |||||||||
Sample |
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Keywords | Drosophila 80S FMRP | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.2 Å | |||||||||
Authors | Chen E / Sharma M R / Shi X / Agrawal R K / Joseph S | |||||||||
Citation | Journal: Mol Cell / Year: 2014 Title: Fragile X mental retardation protein regulates translation by binding directly to the ribosome. Authors: Eileen Chen / Manjuli R Sharma / Xinying Shi / Rajendra K Agrawal / Simpson Joseph / Abstract: Fragile X syndrome (FXS) is the most common form of inherited mental retardation, and it is caused by loss of function of the fragile X mental retardation protein (FMRP). FMRP is an RNA-binding ...Fragile X syndrome (FXS) is the most common form of inherited mental retardation, and it is caused by loss of function of the fragile X mental retardation protein (FMRP). FMRP is an RNA-binding protein that is involved in the translational regulation of several neuronal mRNAs. However, the precise mechanism of translational inhibition by FMRP is unknown. Here, we show that FMRP inhibits translation by binding directly to the L5 protein on the 80S ribosome. Furthermore, cryoelectron microscopic reconstruction of the 80S ribosome⋅FMRP complex shows that FMRP binds within the intersubunit space of the ribosome such that it would preclude the binding of tRNA and translation elongation factors on the ribosome. These findings suggest that FMRP inhibits translation by blocking the essential components of the translational machinery from binding to the ribosome. | |||||||||
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_5805.map.gz | 7.8 MB | EMDB map data format | |
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Header (meta data) | emd-5805-v30.xml emd-5805.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | 400_5805.gif 80_5805.gif | 37 KB 3.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5805 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5805 | HTTPS FTP |
-Validation report
Summary document | emd_5805_validation.pdf.gz | 77.7 KB | Display | EMDB validaton report |
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Full document | emd_5805_full_validation.pdf.gz | 76.8 KB | Display | |
Data in XML | emd_5805_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5805 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5805 | 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_5805.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM reconstruction of Drosophila 80S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.78 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 : Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-F...
Entire | Name: Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-FMRP Complex map) |
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Components |
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-Supramolecule #1000: Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-F...
Supramolecule | Name: Cryo-EM map of the Drosophila 80S Ribosome (control map for 80S-FMRP Complex map) type: sample / ID: 1000 / Details: monodisperse / Number unique components: 1 |
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-Supramolecule #1: 80S ribosome
Supramolecule | Name: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) / synonym: fruit fly / Tissue: embryo / Location in cell: cytoplasm |
Molecular weight | Experimental: 3 MDa / Theoretical: 3 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.12 mg/mL |
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Buffer | pH: 7.7 Details: 50 mM KOAc, 50 mM Tris acetate, pH 7.7, 10 mM DTT, 5 mM Mg(OAc)2 |
Grid | Details: 300 mesh Quantifoil with thin carbon support, glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK II / Method: Blot for 6 seconds before plunging. |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Temperature | Average: 120 K |
Date | Dec 27, 2011 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 102 / Average electron dose: 10 e/Å2 / Bits/pixel: 32 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50760 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: liquid nitrogen-cooled / Specimen holder model: GATAN LIQUID NITROGEN |