+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6549 | |||||||||
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Title | Cryo-EM map of EF4-bound ribosomal complexe | |||||||||
Map data | Reconstruction of POST-EF4 complex | |||||||||
Sample |
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Keywords | ribosome elongation / GTPase EF4 / tRNA back-translocation / P-loop | |||||||||
Function / homology | Function and homology information : / response to pH / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding ...: / response to pH / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / ribosomal small subunit binding / 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 DNA-templated DNA replication initiation / negative regulation of translational initiation / response to salt stress / regulation of mRNA stability / response to cold / 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 / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / positive regulation of translation / response to reactive oxygen species / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / 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 / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Zhang D / Yan K / Liu G / Song G / Luo J / Shi Y / Cheng E / Wu S / Jiang T / Low J ...Zhang D / Yan K / Liu G / Song G / Luo J / Shi Y / Cheng E / Wu S / Jiang T / Low J / Gao N / Qin Y | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2016 Title: EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome. Authors: Dejiu Zhang / Kaige Yan / Guangqiao Liu / Guangtao Song / Jiejian Luo / Yi Shi / Erchao Cheng / Shan Wu / Taijiao Jiang / Jizhong Lou / Ning Gao / Yan Qin / Abstract: EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2- ...EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2-Å resolution, respectively. In Post-EF4, peptidyl-tRNA occupies the peptidyl (P) site, but the interaction between its CCA end and the P loop is disrupted. In Pre-EF4, the peptidyl-tRNA assumes a unique position near the aminoacyl (A) site, denoted the A site/EF4 bound (A/4) site, with a large displacement at its acceptor arm. Mutagenesis analyses suggest that a specific region in the EF4 C-terminal domain (CTD) interferes with base-pairing between the peptidyl-tRNA 3'-CCA and the P loop, whereas the EF4 CTD enhances peptidyl-tRNA interaction at the A/4 site. Therefore, EF4 induces back-translocation by disengaging the tRNA's CCA end from the peptidyl transferase center of the translating ribosome. | |||||||||
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_6549.map.gz | 111.5 MB | EMDB map data format | |
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Header (meta data) | emd-6549-v30.xml emd-6549.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6549_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_6549.tif | 1.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6549 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6549 | HTTPS FTP |
-Validation report
Summary document | emd_6549_validation.pdf.gz | 410.7 KB | Display | EMDB validaton report |
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Full document | emd_6549_full_validation.pdf.gz | 410.2 KB | Display | |
Data in XML | emd_6549_validation.xml.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6549 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6549 | HTTPS FTP |
-Related structure data
Related structure data | 3jcdMC 6550C 3jceC 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_6549.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of POST-EF4 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 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 : Reconstruction of POST-EF4 complex.
Entire | Name: Reconstruction of POST-EF4 complex. |
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Components |
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-Supramolecule #1000: Reconstruction of POST-EF4 complex.
Supramolecule | Name: Reconstruction of POST-EF4 complex. / type: sample / ID: 1000 / Number unique components: 2 |
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-Supramolecule #1: ribosome 70S
Supramolecule | Name: ribosome 70S / 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) |
-Macromolecule #1: EF4
Macromolecule | Name: EF4 / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | 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
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Oct 20, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |