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Yorodumi- EMDB-2008: 3D reconstruction of a translating yeast 80S ribosome in complex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2008 | |||||||||
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Title | 3D reconstruction of a translating yeast 80S ribosome in complex with Dom34p and Rli1p | |||||||||
Map data | This is a 3D cryo-EM reconstruction of a translating yeast 80S ribosome in complex with Dom34p and Rli1p | |||||||||
Sample |
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Keywords | translation / ribosome recycling / no-go mRNA decay | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.2 Å | |||||||||
Authors | 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 | |||||||||
Citation | Journal: Nature / Year: 2012 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2008.map.gz | 26 MB | EMDB map data format | |
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Header (meta data) | emd-2008-v30.xml emd-2008.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
Images | EMBD_2008.gif | 300.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2008 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2008 | HTTPS FTP |
-Validation report
Summary document | emd_2008_validation.pdf.gz | 281.4 KB | Display | EMDB validaton report |
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Full document | emd_2008_full_validation.pdf.gz | 280.6 KB | Display | |
Data in XML | emd_2008_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2008 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2008 | 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_2008.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 3D cryo-EM reconstruction of a translating yeast 80S ribosome in complex with Dom34p and Rli1p | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.17 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 : 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: Saccharomyces cerevisiae (brewer's yeast) / synonym: baker's yeast |
-Macromolecule #1: Rli1p
Macromolecule | Name: Rli1p / type: protein_or_peptide / ID: 1 / Name.synonym: ABCE1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: baker's yeast |
-Macromolecule #2: Dom34p
Macromolecule | Name: Dom34p / type: protein_or_peptide / ID: 2 / Name.synonym: Pelota / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: 10000 / Average electron dose: 25 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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: autoloader / Specimen holder model: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-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 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 |
-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 |