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Yorodumi- EMDB-1430: Specific interaction between EF-G and RRF and its implication for... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1430 | |||||||||
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Title | Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits. | |||||||||
Map data | Cryo-EM map of E.coli 50S complex | |||||||||
Sample |
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Function / homology | Function and homology information cytoplasmic translational termination / ribosome disassembly / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / translational elongation / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...cytoplasmic translational termination / ribosome disassembly / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / translational elongation / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translation elongation factor activity / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.1 Å | |||||||||
Authors | Gao N / Zavialov A / Ehrenberg M / Frank J | |||||||||
Citation | Journal: J Mol Biol / Year: 2007 Title: Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits. Authors: Ning Gao / Andrey V Zavialov / Måns Ehrenberg / Joachim Frank / Abstract: After termination of protein synthesis, the bacterial ribosome is split into its 30S and 50S subunits by the action of ribosome recycling factor (RRF) and elongation factor G (EF-G) in a guanosine 5'- ...After termination of protein synthesis, the bacterial ribosome is split into its 30S and 50S subunits by the action of ribosome recycling factor (RRF) and elongation factor G (EF-G) in a guanosine 5'-triphosphate (GTP)-hydrolysis-dependent manner. Based on a previous cryo-electron microscopy study of ribosomal complexes, we have proposed that the binding of EF-G to an RRF-containing posttermination ribosome triggers an interdomain rotation of RRF, which destabilizes two strong intersubunit bridges (B2a and B3) and, ultimately, separates the two subunits. Here, we present a 9-A (Fourier shell correlation cutoff of 0.5) cryo-electron microscopy map of a 50S x EF-G x guanosine 5'-[(betagamma)-imido]triphosphate x RRF complex and a quasi-atomic model derived from it, showing the interaction between EF-G and RRF on the 50S subunit in the presence of the noncleavable GTP analogue guanosine 5'-[(betagamma)-imido]triphosphate. The detailed information in this model and a comparative analysis of EF-G structures in various nucleotide- and ribosome-bound states show how rotation of the RRF head domain may be triggered by various domains of EF-G. For validation of our structural model, all known mutations in EF-G and RRF that relate to ribosome recycling have been taken into account. More importantly, our results indicate a substantial conformational change in the Switch I region of EF-G, suggesting that a conformational signal transduction mechanism, similar to that employed in transfer RNA translocation on the ribosome by EF-G, translates a large-scale movement of EF-G's domain IV, induced by GTP hydrolysis, into the domain rotation of RRF that eventually splits the ribosome into subunits. | |||||||||
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_1430.map.gz | 7.6 MB | EMDB map data format | |
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Header (meta data) | emd-1430-v30.xml emd-1430.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | 1430.gif | 94.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1430 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1430 | HTTPS FTP |
-Validation report
Summary document | emd_1430_validation.pdf.gz | 308 KB | Display | EMDB validaton report |
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Full document | emd_1430_full_validation.pdf.gz | 307.6 KB | Display | |
Data in XML | emd_1430_validation.xml.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1430 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1430 | HTTPS FTP |
-Related structure data
Related structure data | 2rdoMC 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_1430.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of E.coli 50S complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : 50S subunit with EF-G and RRF bound
Entire | Name: 50S subunit with EF-G and RRF bound |
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Components |
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-Supramolecule #1000: 50S subunit with EF-G and RRF bound
Supramolecule | Name: 50S subunit with EF-G and RRF bound / type: sample / ID: 1000 / Number unique components: 3 |
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-Supramolecule #1: 50S subunit
Supramolecule | Name: 50S subunit / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 |
-Macromolecule #1: EF-G
Macromolecule | Name: EF-G / type: protein_or_peptide / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 |
-Macromolecule #2: RRF
Macromolecule | Name: RRF / type: protein_or_peptide / ID: 2 / Recombinant expression: No |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | Details: Polymix buffer |
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Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Rapid-freezing in liquid ethane / Method: Vitrobot |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 93 K |
Alignment procedure | Legacy - Electron beam tilt params: 0 |
Date | Dec 14, 2007 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 259 / Average electron dose: 15 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 49696 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.9 µm / Nominal defocus min: 1.1 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 |
-Image processing
CTF correction | Details: CTF correctionn of 3D map |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, package / Number images used: 113355 |