+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1915 | |||||||||
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Title | Initial binding position of RRF on the post-termination complex | |||||||||
Map data | E. coli 70S post-termination complex and Thermus thermophilus RRF. | |||||||||
Sample |
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Keywords | ribosome recycling factor / 70S / RRF / T.thermophilus RRF / E.coli 70S / 70S Post Termination Complex / Cryo electron microscopy / cryo-EM / ttRRF | |||||||||
Function / homology | Function and homology information cytoplasmic translational termination / stringent response / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / translational termination / positive regulation of RNA splicing / ribosomal large subunit assembly / maintenance of translational fidelity ...cytoplasmic translational termination / stringent response / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / translational termination / positive regulation of RNA splicing / ribosomal large subunit assembly / maintenance of translational fidelity / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Thermus thermophilus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.1 Å | |||||||||
Authors | Yokoyama T / Shaikh TR / Iwakura N / Kaji H / Kaji A / Agrawal RK | |||||||||
Citation | Journal: EMBO J / Year: 2012 Title: Structural insights into initial and intermediate steps of the ribosome-recycling process. Authors: Takeshi Yokoyama / Tanvir R Shaikh / Nobuhiro Iwakura / Hideko Kaji / Akira Kaji / Rajendra K Agrawal / Abstract: The ribosome-recycling factor (RRF) and elongation factor-G (EF-G) disassemble the 70S post-termination complex (PoTC) into mRNA, tRNA, and two ribosomal subunits. We have determined cryo-electron ...The ribosome-recycling factor (RRF) and elongation factor-G (EF-G) disassemble the 70S post-termination complex (PoTC) into mRNA, tRNA, and two ribosomal subunits. We have determined cryo-electron microscopic structures of the PoTC·RRF complex, with and without EF-G. We find that domain II of RRF initially interacts with universally conserved residues of the 23S rRNA helices 43 and 95, and protein L11 within the 50S ribosomal subunit. Upon EF-G binding, both RRF and tRNA are driven towards the tRNA-exit (E) site, with a large rotational movement of domain II of RRF towards the 30S ribosomal subunit. During this intermediate step of the recycling process, domain II of RRF and domain IV of EF-G adopt hitherto unknown conformations. Furthermore, binding of EF-G to the PoTC·RRF complex reverts the ribosome from ratcheted to unratcheted state. These results suggest that (i) the ribosomal intersubunit reorganizations upon RRF binding and subsequent EF-G binding could be instrumental in destabilizing the PoTC and (ii) the modes of action of EF-G during tRNA translocation and ribosome-recycling steps are markedly different. | |||||||||
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_1915.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-1915-v30.xml emd-1915.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | EMD-1915.tif | 282.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1915 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1915 | HTTPS FTP |
-Validation report
Summary document | emd_1915_validation.pdf.gz | 341.3 KB | Display | EMDB validaton report |
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Full document | emd_1915_full_validation.pdf.gz | 340.9 KB | Display | |
Data in XML | emd_1915_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1915 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1915 | HTTPS FTP |
-Related structure data
Related structure data | 3j0dMC 1916C 1917C 1918C 3j0eC 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_1915.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E. coli 70S post-termination complex and Thermus thermophilus RRF. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.78 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 : T. thermophilus ribosome recycling factor bound to E. coli 70S po...
Entire | Name: T. thermophilus ribosome recycling factor bound to E. coli 70S post-termination complex |
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Components |
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-Supramolecule #1000: T. thermophilus ribosome recycling factor bound to E. coli 70S po...
Supramolecule | Name: T. thermophilus ribosome recycling factor bound to E. coli 70S post-termination complex type: sample / ID: 1000 / Oligomeric state: Heterodimer / Number unique components: 2 |
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Molecular weight | Theoretical: 2.5 MDa |
-Supramolecule #1: 70S Post-Termination Complex
Supramolecule | Name: 70S Post-Termination Complex / type: complex / ID: 1 / Name.synonym: 70S PoTC / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S, SSU 30S |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 2.5 MDa |
-Macromolecule #1: Ribosome-recycling factor
Macromolecule | Name: Ribosome-recycling factor / type: protein_or_peptide / ID: 1 / Name.synonym: RRF / Recombinant expression: Yes |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.08 mg/mL |
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Buffer | pH: 7.5 / Details: 50mM Tris-HCL (pH 7.5), 10mM Mg(OAc)2, 25mM KCl |
Grid | Details: 300 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 80 K |
Alignment procedure | Legacy - Astigmatism: Objective correct at 200kX mag |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 195 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50310 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.3 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen cooled cryo holder Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each micrograph |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Details: CTF correction of 3D maps by Weiner filtration. / Number images used: 153927 |
Final two d classification | Number classes: 83 |
-Atomic model buiding 1
Initial model | PDB ID: 2avy |
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Software | Name: MDFF |
Details | Protocol: Flexible Fitting |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-3j0d: |
-Atomic model buiding 2
Initial model | PDB ID: 2aw4 |
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Software | Name: MDFF |
Details | Protocol: Flexible Fitting |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-3j0d: |