+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1808 | |||||||||
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Title | Yeast 80S ribosome stalled by a stem-loop containing mRNA. | |||||||||
Map data | This is a map of yeast 80S ribosome stalled by a stable 66 nucleotide stem-loop mRNA structure (Hosoda et al., JBC 2003). It contains a P-site tRNA. | |||||||||
Sample |
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Keywords | Ribosome / stalling / mRNA / P-site tRNA / no-go mRNA decay | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.1 Å | |||||||||
Authors | Becker T / Armache JP / Anger AM / Jarasch A / Villa E / Sieber H / AbdelMotaal B / Berninghausen O / Mielke T / Beckmann R | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2011 Title: Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome. Authors: Thomas Becker / Jean-Paul Armache / Alexander Jarasch / Andreas M Anger / Elizabeth Villa / Heidemarie Sieber / Basma Abdel Motaal / Thorsten Mielke / Otto Berninghausen / Roland Beckmann / Abstract: No-go decay (NGD) is a mRNA quality-control mechanism in eukaryotic cells that leads to degradation of mRNAs stalled during translational elongation. The key factors triggering NGD are Dom34 and Hbs1. ...No-go decay (NGD) is a mRNA quality-control mechanism in eukaryotic cells that leads to degradation of mRNAs stalled during translational elongation. The key factors triggering NGD are Dom34 and Hbs1. We used cryo-EM to visualize NGD intermediates resulting from binding of the Dom34-Hbs1 complex to stalled ribosomes. At subnanometer resolution, all domains of Dom34 and Hbs1 were identified, allowing the docking of crystal structures and homology models. Moreover, the close structural similarity of Dom34 and Hbs1 to eukaryotic release factors (eRFs) enabled us to propose a model for the ribosome-bound eRF1-eRF3 complex. Collectively, our data provide structural insights into how stalled mRNA is recognized on the ribosome and how the eRF complex can simultaneously recognize stop codons and catalyze peptide release. | |||||||||
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_1808.map.gz | 16.9 MB | EMDB map data format | |
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Header (meta data) | emd-1808-v30.xml emd-1808.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | EMD-1808.gif | 143.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1808 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1808 | HTTPS FTP |
-Validation report
Summary document | emd_1808_validation.pdf.gz | 246.1 KB | Display | EMDB validaton report |
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Full document | emd_1808_full_validation.pdf.gz | 245.2 KB | Display | |
Data in XML | emd_1808_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1808 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1808 | 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_1808.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a map of yeast 80S ribosome stalled by a stable 66 nucleotide stem-loop mRNA structure (Hosoda et al., JBC 2003). It contains a P-site tRNA. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2375 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 : Stem-loop stalled yeast 80S ribosome
Entire | Name: Stem-loop stalled yeast 80S ribosome |
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Components |
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-Supramolecule #1000: Stem-loop stalled yeast 80S ribosome
Supramolecule | Name: Stem-loop stalled yeast 80S ribosome / type: sample / ID: 1000 / Details: Single particle / Oligomeric state: One ribosome / Number unique components: 1 |
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Molecular weight | Theoretical: 3.2 MDa |
-Supramolecule #1: Saccharomyces cerevisiae 80S ribosome
Supramolecule | Name: Saccharomyces cerevisiae 80S ribosome / type: complex / ID: 1 / Name.synonym: Yeast 80S ribosome Details: The mRNA stem-loop structure is not visible in the Cryo-EM reconstruction indicating its flexibility Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Molecular weight | Experimental: 3.2 MDa / Theoretical: 3.2 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7 Details: 20 mM Tris/HCl, pH 7.0, 80 mM NaCl, 97 mM KOAc, 10 mM Mg(OAc)2, 1.5 mM DTT, 0.02 % Nikkol, 1.8 % Glycerol, 0.01 mg/ml Cycloheximide, 500 0.5 mM GDPNP |
Grid | Details: Quantifoil Grid with 2 nm carbon on top |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot Method: Blotted for 10 seconds before plunging, used 2 layers of filter paper |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Average: 84 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100000 times magnification |
Image recording | Category: CCD / Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 4.76 µm / Number real images: 41 / Average electron dose: 25 e/Å2 Details: Scanned with a Heidelberg PrimeScan drum scanner at 5334 dpi Od range: 1.2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 38000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: FEI Polara Cartridge System / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: CTF correction on the level of 3D volumes (SPIDER TF CTS command) |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 31400 |