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- EMDB-2010: 3D reconstruction of a translating yeast 80S ribosome in complex ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2010 | |||||||||
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Title | 3D reconstruction of a translating yeast 80S ribosome in complex with Dom34p and Rli1p | |||||||||
![]() | This map represents a stalled yeast 80S ribosome in complex with Dom34 and Rli1 before sorting for P-site tRNA. | |||||||||
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![]() | translation / ribosome recycling / no-go mRNA decay | |||||||||
Function / homology | ![]() Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / ribosome disassembly / mTORC1-mediated signalling / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition ...Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / ribosome disassembly / mTORC1-mediated signalling / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / positive regulation of translational initiation / ribosomal subunit export from nucleus / translational termination / RNA endonuclease activity / translational initiation / translation initiation factor activity / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / meiotic cell cycle / ribosomal large subunit biogenesis / positive regulation of translation / small-subunit processome / ribosomal large subunit assembly / cytoplasmic stress granule / rRNA processing / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / iron ion binding / translation / cell division / nucleolus / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.2 Å | |||||||||
![]() | Becker T / Franckenberg S / Wickles S / Shoemaker CJ / Anger AM / Armache J-P / Sieber H / Ungewickell C / Berninghausen O / Daberkow I ...Becker T / Franckenberg S / Wickles S / Shoemaker CJ / Anger AM / Armache J-P / Sieber H / Ungewickell C / Berninghausen O / Daberkow I / Karcher A / Thomm M / Hopfner K-P / Green R / Beckmann R | |||||||||
![]() | ![]() Title: Structural basis of highly conserved ribosome recycling in eukaryotes and archaea. Authors: Thomas Becker / Sibylle Franckenberg / Stephan Wickles / Christopher J Shoemaker / Andreas M Anger / Jean-Paul Armache / Heidemarie Sieber / Charlotte Ungewickell / Otto Berninghausen / Ingo ...Authors: Thomas Becker / Sibylle Franckenberg / Stephan Wickles / Christopher J Shoemaker / Andreas M Anger / Jean-Paul Armache / Heidemarie Sieber / Charlotte Ungewickell / Otto Berninghausen / Ingo Daberkow / Annette Karcher / Michael Thomm / Karl-Peter Hopfner / Rachel Green / Roland Beckmann / ![]() Abstract: Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation ...Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation factor G, and several structures of bacterial recycling complexes have been determined. In the eukaryotic and archaeal kingdoms, however, recycling involves the ABC-type ATPase ABCE1 and little is known about its structural basis. Here we present cryo-electron microscopy reconstructions of eukaryotic and archaeal ribosome recycling complexes containing ABCE1 and the termination factor paralogue Pelota. These structures reveal the overall binding mode of ABCE1 to be similar to canonical translation factors. Moreover, the iron-sulphur cluster domain of ABCE1 interacts with and stabilizes Pelota in a conformation that reaches towards the peptidyl transferase centre, thus explaining how ABCE1 may stimulate peptide-release activity of canonical termination factors. Using the mechanochemical properties of ABCE1, a conserved mechanism in archaea and eukaryotes is suggested that couples translation termination to recycling, and eventually to re-initiation. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 23.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13 KB 13 KB | Display Display | ![]() |
Images | ![]() | 238 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 369.6 KB | Display | ![]() |
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Full document | ![]() | 369.1 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3j16MC ![]() 2008C ![]() 2009C ![]() 3j15C M: atomic model generated by this map 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 | This map represents a stalled yeast 80S ribosome in complex with Dom34 and Rli1 before sorting for 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
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Sample components
-Entire : Saccharomyces cerevisiae 80S ribosome stalled by a synthetic stem...
Entire | Name: Saccharomyces cerevisiae 80S ribosome stalled by a synthetic stem-loop mRNA in complex with Dom34p and Rli1p |
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Components |
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-Supramolecule #1000: Saccharomyces cerevisiae 80S ribosome stalled by a synthetic stem...
Supramolecule | Name: Saccharomyces cerevisiae 80S ribosome stalled by a synthetic stem-loop mRNA in complex with Dom34p and Rli1p type: sample / ID: 1000 Oligomeric state: One 80S ribosome binds one Dom34p and one Rli1p Number unique components: 3 |
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-Supramolecule #1: S. cerevisiae 80S ribosome
Supramolecule | Name: S. cerevisiae 80S ribosome / type: complex / ID: 1 / Name.synonym: Baker's yeast 80S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Rli1p
Macromolecule | Name: Rli1p / type: protein_or_peptide / ID: 1 / Name.synonym: ABCE1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #2: Dom34p
Macromolecule | Name: Dom34p / type: protein_or_peptide / ID: 2 / Name.synonym: Pelota / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 Details: 20 mM Tris/HCl pH 7.0, 150 mM KOAc, 10 mM Mg(OAc)2, 1.5 mM DTT, 0.005% Nikkol, 0.01 mg/ml Cycloheximide, 0.3% (w/v) Digitonin, 0.5 mM ADPNP |
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Grid | Details: Quantifoil grids (3/3) with 2 nm carbon on top |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot Method: Blot for 10 seconds before plunging, use 2 layer of filter paper |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | Final magnification of the object on the CCD image is 128200 |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 5610 / Average electron dose: 25 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder: Dual tilt autoloader cartridge / Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Details | mammalian Sec61 complex was added to saturate hydrophobic nascent polypeptide chains |
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CTF correction | Details: Wiener Filter |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER Details: sorting for ribosome conformation and ligand presence was performed. This map represents the step after sorting for ligand presence but before sorting for p_site tRNA. Number images used: 45700 |
Final angle assignment | Details: SPIDER |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: 0 |
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Software | Name: MDFF |
Details | PDBEntryID_givenInChain. Protocol: rigid body followed by molecular dynamics flexible fitting. rigid body fitting of individual domains followed by molecular dynamics flexible fitting |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-3j16: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: MDFF |
Details | PDBEntryID_givenInChain. Protocol: rigid body followed by molecular dynamics flexible fitting. rigid body followed by molecular dynamics flexible fitting |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-3j16: |