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Yorodumi- PDB-3j16: Models of ribosome-bound Dom34p and Rli1p and their ribosomal bin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3j16 | ||||||
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Title | Models of ribosome-bound Dom34p and Rli1p and their ribosomal binding partners | ||||||
Components |
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Keywords | RIBOSOME / ribosome recycling / translation / eukarya | ||||||
Function / homology | Function and homology information 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 / ribosomal subunit export from nucleus / 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 / 90S preribosome / 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) / ribosomal small subunit binding / positive regulation of translational initiation / L13a-mediated translational silencing of Ceruloplasmin expression / translational termination / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational initiation / rescue of stalled ribosome / RNA endonuclease activity / translation initiation factor activity / ribosomal large subunit biogenesis / meiotic cell cycle / small-subunit processome / positive regulation of translation / cytoplasmic stress granule / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / translation / iron ion binding / cell division / nucleolus / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å | ||||||
Authors | Becker, T. / Franckenberg, S. / Wickles, S. / Shoemaker, C.J. / Anger, A.M. / Armache, J.-P. / Sieber, H. / Ungewickell, C. / Berninghausen, O. / Daberkow, I. ...Becker, T. / Franckenberg, S. / Wickles, S. / Shoemaker, C.J. / Anger, A.M. / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j16.cif.gz | 611.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j16.ent.gz | 447.5 KB | Display | PDB format |
PDBx/mmJSON format | 3j16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/3j16 ftp://data.pdbj.org/pub/pdb/validation_reports/j1/3j16 | HTTPS FTP |
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-Related structure data
Related structure data | 2010MC 2008C 2009C 3j15C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 44119.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33309 |
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#2: Protein | Mass: 68433.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03195 |
-RNA chain , 3 types, 3 molecules JKL
#3: RNA chain | Mass: 75106.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
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#4: RNA chain | Mass: 49863.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
#5: RNA chain | Mass: 24135.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
-60S ribosomal protein ... , 3 types, 3 molecules FGH
#6: Protein | Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05738 |
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#8: Protein | Mass: 33749.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05317 |
#10: Protein | Mass: 17850.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX53 |
-40S ribosomal protein ... , 4 types, 4 molecules ECID
#7: Protein | Mass: 7137.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX33 |
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#9: Protein | Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX37 |
#11: Protein | Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX41 |
#12: Protein | Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CX31 |
-Non-polymers , 4 types, 5 molecules
#13: Chemical | ChemComp-MG / | ||
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#14: Chemical | ChemComp-ATP / | ||
#15: Chemical | #16: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Dom34p-Rli1p complex / Type: COMPLEX |
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Buffer solution | 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 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 95 % / Details: ethane (Vitrobot) |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1400 nm |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
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3D reconstruction | Method: Single particleSingle particle analysis / Resolution: 7.2 Å / Num. of particles: 45700 / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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