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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12988 | ||||||||||||
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Title | rancRNA_18 processing and classification | ||||||||||||
![]() | postrpocessed map 60s all particles | ||||||||||||
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Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||||||||
![]() | Zuber B / Iacovache I | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 27.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.6 KB 19.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16 KB | Display | ![]() |
Images | ![]() | 68.3 KB | ||
Others | ![]() ![]() ![]() ![]() | 274.5 MB 273.6 MB 273.8 MB 273.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | postrpocessed map 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: refinement of Class 4 after 2D classification
File | emd_12988_additional_1.map | ||||||||||||
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Annotation | refinement of Class 4 after 2D classification | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: refinement 80S all particles
File | emd_12988_additional_2.map | ||||||||||||
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Annotation | refinement 80S all particles | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: refinement of Class 7 after 2D classification
File | emd_12988_additional_3.map | ||||||||||||
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Annotation | refinement of Class 7 after 2D classification | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: refinement of Class 5 after 2D classification
File | emd_12988_additional_4.map | ||||||||||||
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Annotation | refinement of Class 5 after 2D classification | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : rancRNA_18 treated sample - cryoEM analysis and classification
Entire | Name: rancRNA_18 treated sample - cryoEM analysis and classification |
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Components |
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-Supramolecule #1: rancRNA_18 treated sample - cryoEM analysis and classification
Supramolecule | Name: rancRNA_18 treated sample - cryoEM analysis and classification type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |