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Yorodumi- EMDB-5800: Structure of the Ribosome with Elongation Factor G Trapped in the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5800 | |||||||||
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Title | Structure of the Ribosome with Elongation Factor G Trapped in the Pre-Translocation State | |||||||||
Map data | Reconstruction of a pre-translocation ribosome with EF-G bound | |||||||||
Sample |
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Keywords | protein structure / translation / EF-G / electron cryo-microscopy / single particle analysis | |||||||||
Function / homology | Function and homology information intracellular anatomical structure / ribosome disassembly / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / translational elongation / RNA folding ...intracellular anatomical structure / ribosome disassembly / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / translational elongation / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translation elongation factor activity / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / maintenance of translational fidelity / response to radiation / 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 / cytoplasmic translation / tRNA binding / molecular adaptor activity / 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 / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.6 Å | |||||||||
Authors | Brilot AF / Korostelev AA / Ermolenko DN / Grigorieff N | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2013 Title: Structure of the ribosome with elongation factor G trapped in the pretranslocation state. Authors: Axel F Brilot / Andrei A Korostelev / Dmitri N Ermolenko / Nikolaus Grigorieff / Abstract: During protein synthesis, tRNAs and their associated mRNA codons move sequentially on the ribosome from the A (aminoacyl) site to the P (peptidyl) site to the E (exit) site in a process catalyzed by ...During protein synthesis, tRNAs and their associated mRNA codons move sequentially on the ribosome from the A (aminoacyl) site to the P (peptidyl) site to the E (exit) site in a process catalyzed by a universally conserved ribosome-dependent GTPase [elongation factor G (EF-G) in prokaryotes and elongation factor 2 (EF-2) in eukaryotes]. Although the high-resolution structure of EF-G bound to the posttranslocation ribosome has been determined, the pretranslocation conformation of the ribosome bound with EF-G and A-site tRNA has evaded visualization owing to the transient nature of this state. Here we use electron cryomicroscopy to determine the structure of the 70S ribosome with EF-G, which is trapped in the pretranslocation state using antibiotic viomycin. Comparison with the posttranslocation ribosome shows that the small subunit of the pretranslocation ribosome is rotated by ∼12° relative to the large subunit. Domain IV of EF-G is positioned in the cleft between the body and head of the small subunit outwardly of the A site and contacts the A-site tRNA. Our findings suggest a model in which domain IV of EF-G promotes the translocation of tRNA from the A to the P site as the small ribosome subunit spontaneously rotates back from the hybrid, rotated state into the nonrotated posttranslocation state. | |||||||||
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_5800.map.gz | 104.8 MB | EMDB map data format | |
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Header (meta data) | emd-5800-v30.xml emd-5800.xml | 19 KB 19 KB | Display Display | EMDB header |
Images | emd_5800_1.jpg emd_5800_2.png | 199.8 KB 230.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5800 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5800 | HTTPS FTP |
-Validation report
Summary document | emd_5800_validation.pdf.gz | 355.7 KB | Display | EMDB validaton report |
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Full document | emd_5800_full_validation.pdf.gz | 355.2 KB | Display | |
Data in XML | emd_5800_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5800 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5800 | HTTPS FTP |
-Related structure data
Related structure data | 4v7dMC 5796C 5797C 5798C 5799C 4v7cC C: citing same article (ref.) M: atomic model generated by this map |
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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_5800.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of a pre-translocation ribosome with EF-G bound | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 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 : Pre-translocation 70S ribosome with bound EF-G and bound A/P* and...
Entire | Name: Pre-translocation 70S ribosome with bound EF-G and bound A/P* and P/E hybrid state tRNA |
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Components |
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-Supramolecule #1000: Pre-translocation 70S ribosome with bound EF-G and bound A/P* and...
Supramolecule | Name: Pre-translocation 70S ribosome with bound EF-G and bound A/P* and P/E hybrid state tRNA type: sample / ID: 1000 / Details: Sample was monodisperse / Number unique components: 5 |
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Molecular weight | Theoretical: 3 MDa |
-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 |
Molecular weight | Theoretical: 3 MDa |
-Macromolecule #1: Elongation Factor G
Macromolecule | Name: Elongation Factor G / type: protein_or_peptide / ID: 1 / Name.synonym: EF-G / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K-12 |
Molecular weight | Theoretical: 78 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: pET24b |
Sequence | UniProtKB: Elongation factor G GO: translational elongation, GTP binding, translation elongation factor activity, intracellular anatomical structure InterPro: Translation elongation factor EFG/EF2 |
-Macromolecule #2: Transfer RNA
Macromolecule | Name: Transfer RNA / type: rna / ID: 2 / Name.synonym: tRNA / Details: Two tRNA (P and E site) / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K-12 |
Molecular weight | Experimental: 25 KDa |
-Macromolecule #3: Messenger RNA
Macromolecule | Name: Messenger RNA / type: rna / ID: 3 / Name.synonym: mRNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 12 KDa |
Sequence | String: GGCAAGGAGG UAAAAAUGUU UAAACGUAAA UCUACU |
-Macromolecule #4: Viomycin
Macromolecule | Name: Viomycin / type: ligand / ID: 4 / Name.synonym: Vio / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 1 KDa |
Chemical component information |
ChemComp-PRD_000226: |