+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2183 | |||||||||
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Title | Structural basis for TetM-mediated tetracycline resistance | |||||||||
Map data | Cryo EM reconstruction of an E. coli 70S ribosome bound to ribosome protection protein TetM | |||||||||
Sample |
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Keywords | antibiotics / protein synthesis / resistance / ribosome / TetM / tetracycline / tigecycline / translation | |||||||||
Function / homology | Function and homology information ribosome disassembly / translation / response to antibiotic / GTPase activity / GTP binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Enterococcus faecalis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.2 Å | |||||||||
Authors | Doenhoefer A / Franckenberg S / Wickles S / Berninghausen O / Beckmann R / Wilson DN | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Structural basis for TetM-mediated tetracycline resistance. Authors: Alexandra Dönhöfer / Sibylle Franckenberg / Stephan Wickles / Otto Berninghausen / Roland Beckmann / Daniel N Wilson / Abstract: Ribosome protection proteins (RPPs) confer tetracycline resistance by binding to the ribosome and chasing the drug from its binding site. The current model for the mechanism of action of RPPs ...Ribosome protection proteins (RPPs) confer tetracycline resistance by binding to the ribosome and chasing the drug from its binding site. The current model for the mechanism of action of RPPs proposes that drug release is indirect and achieved via conformational changes within the drug-binding site induced upon binding of the RPP to the ribosome. Here we report a cryo-EM structure of the RPP TetM in complex with the 70S ribosome at 7.2-Å resolution. The structure reveals the contacts of TetM with the ribosome, including interaction between the conserved and functionally critical C-terminal extension of TetM and the decoding center of the small subunit. Moreover, we observe direct interaction between domain IV of TetM and the tetracycline binding site and identify residues critical for conferring tetracycline resistance. A model is presented whereby TetM directly dislodges tetracycline to confer resistance. | |||||||||
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_2183.map.gz | 18.8 MB | EMDB map data format | |
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Header (meta data) | emd-2183-v30.xml emd-2183.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | EMD-2183.png | 165.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2183 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2183 | HTTPS FTP |
-Validation report
Summary document | emd_2183_validation.pdf.gz | 354.8 KB | Display | EMDB validaton report |
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Full document | emd_2183_full_validation.pdf.gz | 354.4 KB | Display | |
Data in XML | emd_2183_validation.xml.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2183 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2183 | HTTPS FTP |
-Related structure data
Related structure data | 3j25MC 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_2183.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo EM reconstruction of an E. coli 70S ribosome bound to ribosome protection protein TetM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2374 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 : Escherichia coli 70S ribosome in complex with ribosome protection...
Entire | Name: Escherichia coli 70S ribosome in complex with ribosome protection protein TetM |
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Components |
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-Supramolecule #1000: Escherichia coli 70S ribosome in complex with ribosome protection...
Supramolecule | Name: Escherichia coli 70S ribosome in complex with ribosome protection protein TetM type: sample / ID: 1000 / Number unique components: 2 |
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-Supramolecule #1: Escherichia coli 70S ribosome
Supramolecule | Name: Escherichia coli 70S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Tetracycline resistance protein TetM
Macromolecule | Name: Tetracycline resistance protein TetM / type: protein_or_peptide / ID: 1 / Name.synonym: TetM / Recombinant expression: No |
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Source (natural) | Organism: Enterococcus faecalis (bacteria) |
Sequence | UniProtKB: Tetracycline resistance protein TetM from transposon Tn916 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 / Details: 20mM Hepes-KOH pH 7.8, 30 mM NH4Cl and 10 mM MgCl2 |
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Grid | Details: Quantifoil grids (3/3) with 2 nm carbon on top |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV Method: Blot for 10 seconds before plunging, used 2 layers of filter paper |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Jul 1, 2011 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -3.5 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER Details: Sorting for ribosome conformation and ligand presence was performed Number images used: 52701 |
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