+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12986 | ||||||||||||
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Title | Control sample rancRNA_18 | ||||||||||||
Map data | postrpocessed 60S all particles | ||||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.1 Å | ||||||||||||
Authors | Zuber B / Iacovache I | ||||||||||||
Funding support | Switzerland, 3 items
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Citation | Journal: RNA Biol / Year: 2021 Title: A small ribosome-associated ncRNA globally inhibits translation by restricting ribosome dynamics. Authors: Julia Reuther / Lukas Schneider / Ioan Iacovache / Andreas Pircher / Walid H Gharib / Benoît Zuber / Norbert Polacek / Abstract: Ribosome-associated non-coding RNAs (rancRNAs) have been recognized as an emerging class of regulatory molecules capable of fine-tuning translation in all domains of life. RancRNAs are ideally suited ...Ribosome-associated non-coding RNAs (rancRNAs) have been recognized as an emerging class of regulatory molecules capable of fine-tuning translation in all domains of life. RancRNAs are ideally suited for allowing a swift response to changing environments and are therefore considered pivotal during the first wave of stress adaptation. Previously, we identified an mRNA-derived 18 nucleotides long rancRNA (rancRNA_18) in that rapidly downregulates protein synthesis during hyperosmotic stress. However, the molecular mechanism of action remained enigmatic. Here, we combine biochemical, genetic, transcriptome-wide and structural evidence, thus revealing rancRNA_18 as global translation inhibitor by targeting the E-site region of the large ribosomal subunit. Ribosomes carrying rancRNA_18 possess decreased affinity for A-site tRNA and impaired structural dynamics. Cumulatively, these discoveries reveal the mode of action of a rancRNA involved in modulating protein biosynthesis at a thus far unequalled precision. | ||||||||||||
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_12986.map.gz | 25.4 MB | EMDB map data format | |
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Header (meta data) | emd-12986-v30.xml emd-12986.xml | 21.4 KB 21.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12986_fsc.xml | 16.1 KB | Display | FSC data file |
Images | emd_12986.png | 82.4 KB | ||
Others | emd_12986_additional_1.map.gz emd_12986_additional_2.map.gz emd_12986_additional_3.map.gz emd_12986_additional_4.map.gz emd_12986_additional_5.map.gz | 274.1 MB 275.6 MB 274.8 MB 275 MB 273.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12986 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12986 | HTTPS FTP |
-Validation report
Summary document | emd_12986_validation.pdf.gz | 344.8 KB | Display | EMDB validaton report |
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Full document | emd_12986_full_validation.pdf.gz | 344.4 KB | Display | |
Data in XML | emd_12986_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | emd_12986_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12986 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12986 | HTTPS FTP |
-Related structure data
Related structure data | 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_12986.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | postrpocessed 60S all particles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.052 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: 2D classification C5
File | emd_12986_additional_1.map | ||||||||||||
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Annotation | 2D classification C5 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 2D classification C6
File | emd_12986_additional_2.map | ||||||||||||
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Annotation | 2D classification C6 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Refinement 80s all particles
File | emd_12986_additional_3.map | ||||||||||||
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Annotation | Refinement 80s all particles | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 2D classification C10
File | emd_12986_additional_4.map | ||||||||||||
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Annotation | 2D classification C10 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 2D classification C8
File | emd_12986_additional_5.map | ||||||||||||
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Annotation | 2D classification C8 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : control sample for rancRNA_18 - cryoEM analysis and classification
Entire | Name: control sample for rancRNA_18 - cryoEM analysis and classification |
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Components |
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-Supramolecule #1: control sample for rancRNA_18 - cryoEM analysis and classification
Supramolecule | Name: control sample for rancRNA_18 - cryoEM analysis and classification type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: trm10d |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | |||||||||||||||
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Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.25 mm / Nominal magnification: 100000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |