+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5562 | |||||||||
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Title | tetracycline resistance protein Tet(O) bound to the ribosome | |||||||||
Map data | 70S ribosome from E. coli | |||||||||
Sample |
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Keywords | 70S ribosome / antibiotic resistance / cryo-electron microscopy | |||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / stringent response / 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 ...negative regulation of cytoplasmic translational initiation / stringent response / 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 / 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 / translational initiation / regulation of cell growth / DNA-templated transcription termination / 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 / 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: 9.8 Å | |||||||||
Authors | Li W / Atkinson GC / Thakor NS / Allas U / Lu C / Chan KY / Tenson T / Schulten K / Wilson KS / Hauryliuk V / Frank J | |||||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Mechanism of tetracycline resistance by ribosomal protection protein Tet(O). Authors: Wen Li / Gemma C Atkinson / Nehal S Thakor / Ular Allas / Chuao-chao Lu / Kwok-Yan Chan / Tanel Tenson / Klaus Schulten / Kevin S Wilson / Vasili Hauryliuk / Joachim Frank / Abstract: Tetracycline resistance protein Tet(O), which protects the bacterial ribosome from binding the antibiotic tetracycline, is a translational GTPase with significant similarity in both sequence and ...Tetracycline resistance protein Tet(O), which protects the bacterial ribosome from binding the antibiotic tetracycline, is a translational GTPase with significant similarity in both sequence and structure to the elongation factor EF-G. Here, we present an atomic model of the Tet(O)-bound 70S ribosome based on our cryo-electron microscopic reconstruction at 9.6-Å resolution. This atomic model allowed us to identify the Tet(O)-ribosome binding sites, which involve three characteristic loops in domain 4 of Tet(O). Replacements of the three amino-acid tips of these loops by a single glycine residue result in loss of Tet(O)-mediated tetracycline resistance. On the basis of these findings, the mechanism of Tet(O)-mediated tetracycline resistance can be explained in molecular detail. | |||||||||
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_5562.map.gz | 8.7 MB | EMDB map data format | |
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Header (meta data) | emd-5562-v30.xml emd-5562.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | emd_5562_1.jpg | 94.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5562 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5562 | HTTPS FTP |
-Validation report
Summary document | emd_5562_validation.pdf.gz | 343.6 KB | Display | EMDB validaton report |
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Full document | emd_5562_full_validation.pdf.gz | 343.2 KB | Display | |
Data in XML | emd_5562_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5562 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5562 | HTTPS FTP |
-Related structure data
Related structure data | 4v6vMC 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_5562.map.gz / Format: CCP4 / Size: 9.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 70S ribosome from E. coli | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.71 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 : 70S-Tet(O)
Entire | Name: 70S-Tet(O) |
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Components |
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-Supramolecule #1000: 70S-Tet(O)
Supramolecule | Name: 70S-Tet(O) / type: sample / ID: 1000 / Number unique components: 1 |
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-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) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK I |
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-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Oct 18, 2010 |
Image recording | Number real images: 98000 / Average electron dose: 10 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: GATAN HELIUM |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: group defocus |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 9.8 Å / Resolution method: OTHER / Software - Name: SPIDER / Number images used: 98000 |