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Yorodumi- EMDB-9531: Cryo-EM structure of the model post-termination complex (PoTC) in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9531 | |||||||||
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Title | Cryo-EM structure of the model post-termination complex (PoTC) in the unrotated state | |||||||||
Map data | Model post-termination complex (PoTC) in the unratcheted state | |||||||||
Sample |
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Function / homology | Function and homology information stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.4 Å | |||||||||
Authors | Iwakura N / Yokoyama T / Quaglia F / Mitsuoka K / Mio K / Shigematsu H / Shirouzu M / Kaji A / Kaji H | |||||||||
Citation | Journal: PLoS One / Year: 2017 Title: Chemical and structural characterization of a model Post-Termination Complex (PoTC) for the ribosome recycling reaction: Evidence for the release of the mRNA by RRF and EF-G. Authors: Nobuhiro Iwakura / Takeshi Yokoyama / Fabio Quaglia / Kaoru Mitsuoka / Kazuhiro Mio / Hideki Shigematsu / Mikako Shirouzu / Akira Kaji / Hideko Kaji / Abstract: A model Post-Termination Complex (PoTC) used for the discovery of Ribosome Recycling Factor (RRF) was purified and characterized by cryo-electron microscopic analysis and biochemical methods. We ...A model Post-Termination Complex (PoTC) used for the discovery of Ribosome Recycling Factor (RRF) was purified and characterized by cryo-electron microscopic analysis and biochemical methods. We established that the model PoTC has mostly one tRNA, at the P/E or P/P position, together with one mRNA. The structural studies were supported by the biochemical measurement of bound tRNA and mRNA. Using this substrate, we establish that the release of tRNA, release of mRNA and splitting of ribosomal subunits occur during the recycling reaction. Order of these events is tRNA release first followed by mRNA release and splitting almost simultaneously. Moreover, we demonstrate that IF3 is not involved in any of the recycling reactions but simply prevents the re-association of split ribosomal subunits. Our finding demonstrates that the important function of RRF includes the release of mRNA, which is often missed by the use of a short ORF with the Shine-Dalgarno sequence near the termination site. | |||||||||
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_9531.map.gz | 88.3 MB | EMDB map data format | |
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Header (meta data) | emd-9531-v30.xml emd-9531.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | emd_9531.png | 800.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9531 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9531 | HTTPS FTP |
-Validation report
Summary document | emd_9531_validation.pdf.gz | 430.3 KB | Display | EMDB validaton report |
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Full document | emd_9531_full_validation.pdf.gz | 429.9 KB | Display | |
Data in XML | emd_9531_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_9531_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9531 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9531 | 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_9531.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Model post-termination complex (PoTC) in the unratcheted state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.22 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 : Model post-termination complex (PoTC)
Entire | Name: Model post-termination complex (PoTC) |
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Components |
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-Supramolecule #1: Model post-termination complex (PoTC)
Supramolecule | Name: Model post-termination complex (PoTC) / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL 3100FFC |
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Image recording | Film or detector model: KODAK SO-163 FILM / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 20673 |
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Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2) |