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- EMDB-1128: Mechanism for the disassembly of the posttermination complex infe... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1128 | |||||||||
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Title | Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. | |||||||||
![]() | This is a 70S.tRNA(Ile).mRNA.puromycin.RRF complex from E.coli | |||||||||
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Function / homology | ![]() cytoplasmic translational termination / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding ...cytoplasmic translational termination / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 14.1 Å | |||||||||
![]() | Gao N / Zavialov AV / Li W / Sengupta J / Valle M / Gursky RP / Ehrenberg M / Frank J | |||||||||
![]() | ![]() Title: Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Authors: Ning Gao / Andrey V Zavialov / Wen Li / Jayati Sengupta / Mikel Valle / Richard P Gursky / Måns Ehrenberg / Joachim Frank / ![]() Abstract: Ribosome recycling, the disassembly of the posttermination complex after each round of protein synthesis, is an essential step in mRNA translation, but its mechanism has remained obscure. In ...Ribosome recycling, the disassembly of the posttermination complex after each round of protein synthesis, is an essential step in mRNA translation, but its mechanism has remained obscure. In eubacteria, recycling is catalyzed by RRF (ribosome recycling factor) and EF-G (elongation factor G). By using cryo-electron microscopy, we have obtained two density maps, one of the RRF bound posttermination complex and one of the 50S subunit bound with both EF-G and RRF. Comparing the two maps, we found domain I of RRF to be in the same orientation, while domain II in the EF-G-containing 50S subunit is extensively rotated (approximately 60 degrees) compared to its orientation in the 70S complex. Mapping the 50S conformation of RRF onto the 70S posttermination complex suggests that it can disrupt the intersubunit bridges B2a and B3, and thus effect a separation of the two subunits. These observations provide the structural basis for the mechanism by which the posttermination complex is split into subunits by the joint action of RRF and EF-G. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.2 KB 10.2 KB | Display Display | ![]() |
Images | ![]() | 20.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zn0MC ![]() 1zn1MC ![]() 1127C 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a 70S.tRNA(Ile).mRNA.puromycin.RRF complex from E.coli | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.82 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 : 70S.tRNA-Ile.mRNA.puromycin.RRF from E.coli ribosome
Entire | Name: 70S.tRNA-Ile.mRNA.puromycin.RRF from E.coli ribosome |
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Components |
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-Supramolecule #1000: 70S.tRNA-Ile.mRNA.puromycin.RRF from E.coli ribosome
Supramolecule | Name: 70S.tRNA-Ile.mRNA.puromycin.RRF from E.coli ribosome / type: sample / ID: 1000 / Number unique components: 4 |
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-Supramolecule #1: 70S
Supramolecule | Name: 70S / type: complex / ID: 1 / Ribosome-details: ribosome-prokaryote: ALL |
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-Macromolecule #1: RRF
Macromolecule | Name: RRF / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No |
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-Macromolecule #2: tRNA-ILE
Macromolecule | Name: tRNA-ILE / type: rna / ID: 2 / Classification: TRANSFER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #3: mRNA
Macromolecule | Name: mRNA / type: other / ID: 3 / Classification: DNA/RNA / Structure: SINGLE STRANDED / Synthetic?: Yes |
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-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 / Details: polymix buffer |
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Staining | Type: NEGATIVE / Details: Cryo-EM |
Grid | Details: Quantifoil holley carbon film grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: two-sided blotting plunger Method: Blot for 2 seconds before plunging |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 93 K |
Date | Feb 1, 2003 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Average electron dose: 15 e/Å2 / Od range: 1.2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 49700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: defocus groups |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER Details: Amplitude correction was applied using low-angle x-ray scattering data. Number images used: 37379 |