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Yorodumi- EMDB-2009: 3D reconstruction of an archaeal 70S ribosome in complex with aPe... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2009 | |||||||||
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Title | 3D reconstruction of an archaeal 70S ribosome in complex with aPelota and aABCE1 | |||||||||
Map data | This is a 3D cryo-EM reconstruction of a Pyrococcus furiosus 70S ribosome in complex with aABCE1 and aPelota | |||||||||
Sample |
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Keywords | translation / ribosome recycling / no-go mRNA decay | |||||||||
Function / homology | Function and homology information RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / ribonuclease P activity / tRNA 5'-leader removal / ribosome disassembly / nonfunctional rRNA decay / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis ...RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / ribonuclease P activity / tRNA 5'-leader removal / ribosome disassembly / nonfunctional rRNA decay / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / rRNA processing / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / endonuclease activity / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / Hydrolases; Acting on ester bonds / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Pyrococcus furiosus (archaea) / Thermococcus kodakarensis (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 6.6 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_2009.map.gz | 23.1 MB | EMDB map data format | |
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Header (meta data) | emd-2009-v30.xml emd-2009.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | EMBD_2009.gif | 551.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2009 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2009 | HTTPS FTP |
-Validation report
Summary document | emd_2009_validation.pdf.gz | 373.1 KB | Display | EMDB validaton report |
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Full document | emd_2009_full_validation.pdf.gz | 372.7 KB | Display | |
Data in XML | emd_2009_validation.xml.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2009 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2009 | HTTPS FTP |
-Related structure data
Related structure data | 3j15MC 4v6uM 2008C 2010C 3j16C M: atomic model generated by this map 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_2009.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 Pyrococcus furiosus 70S ribosome in complex with aABCE1 and aPelota | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Pyrococcus furiosus 70S ribosome in complex with aPelota and aABCE1
Entire | Name: Pyrococcus furiosus 70S ribosome in complex with aPelota and aABCE1 |
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Components |
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-Supramolecule #1000: Pyrococcus furiosus 70S ribosome in complex with aPelota and aABCE1
Supramolecule | Name: Pyrococcus furiosus 70S ribosome in complex with aPelota and aABCE1 type: sample / ID: 1000 Oligomeric state: One 70S ribosome binds one aPelota and one aABCE1 Number unique components: 3 |
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-Supramolecule #1: Pyrococcus furiosus 70S ribosome
Supramolecule | Name: Pyrococcus furiosus 70S ribosome / type: complex / ID: 1 / Name.synonym: Pyrococcus furiosus 70S ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Pyrococcus furiosus (archaea) |
-Macromolecule #1: aABCE1
Macromolecule | Name: aABCE1 / type: protein_or_peptide / ID: 1 / Name.synonym: ABCE1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Pyrococcus furiosus (archaea) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #2: aPelota
Macromolecule | Name: aPelota / type: protein_or_peptide / ID: 2 / Name.synonym: Pelota / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Thermococcus kodakarensis (archaea) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET28 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8.2 Details: 56 mM Tris pH 8.2, 250 mM KOAc, 80 mM NH4OAc, 50 mM MgCl2, 1 mM DTT, 2 mM ADPNP |
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Staining | Type: NEGATIVE / Details: cryo-EM |
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 148721 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 10000 / Average electron dose: 25 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder: autoloader / Specimen holder model: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Wiener Filter |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER Details: sorting for ribosome conformation and ligand presence was performed Number images used: 51000 |
Final angle assignment | Details: SPIDER |
-Atomic model buiding 1
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 fitting of individual domains followed by molecular dynamics flexible fitting |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-3j15: PDB-4v6u: |