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- PDB-6spb: Pseudomonas aeruginosa 50s ribosome from a clinical isolate with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6spb | |||||||||||||||
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Title | Pseudomonas aeruginosa 50s ribosome from a clinical isolate with a mutation in uL6 | |||||||||||||||
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![]() | RIBOSOME / Pseudomonas aeruginosa / mutation | |||||||||||||||
Function / homology | ![]() large ribosomal subunit / 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 ...large ribosomal subunit / 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 / ribonucleoprotein complex / translation / mRNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å | |||||||||||||||
![]() | Halfon, Y. / Jimenez-Fernande, A. / La Ros, R. / Espinos, R. / Krogh Johansen, H. / Matzov, D. / Eyal, Z. / Bashan, A. / Zimmerman, E. / Belousoff, M. ...Halfon, Y. / Jimenez-Fernande, A. / La Ros, R. / Espinos, R. / Krogh Johansen, H. / Matzov, D. / Eyal, Z. / Bashan, A. / Zimmerman, E. / Belousoff, M. / Molin, S. / Yonath, A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of ribosomes from an aminoglycoside-resistant clinical isolate. Authors: Yehuda Halfon / Alicia Jimenez-Fernandez / Ruggero La Rosa / Rocio Espinosa Portero / Helle Krogh Johansen / Donna Matzov / Zohar Eyal / Anat Bashan / Ella Zimmerman / Matthew Belousoff / ...Authors: Yehuda Halfon / Alicia Jimenez-Fernandez / Ruggero La Rosa / Rocio Espinosa Portero / Helle Krogh Johansen / Donna Matzov / Zohar Eyal / Anat Bashan / Ella Zimmerman / Matthew Belousoff / Søren Molin / Ada Yonath / ![]() ![]() ![]() Abstract: Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a ...Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a major target for clinically useful antibiotics. We report here the cryo-electron microscopy structures of the ribosome of a pathogenic aminoglycoside (AG)-resistant strain, as well as of a nonresistance strain isolated from a cystic fibrosis patient. The structural studies disclosed defective ribosome complex formation due to a conformational change of rRNA helix H69, an essential intersubunit bridge, and a secondary binding site of the AGs. In addition, a stable conformation of nucleotides A1486 and A1487, pointing into helix h44, is created compared to a non-AG-bound ribosome. We suggest that altering the conformations of ribosomal protein uL6 and rRNA helix H69, which interact with initiation-factor IF2, interferes with proper protein synthesis initiation. | |||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 10280MC ![]() 6spcC ![]() 6spdC ![]() 6speC ![]() 6spfC ![]() 6spgC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 2 types, 2 molecules AB
#1: RNA chain | Mass: 935990.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: RNA chain | Mass: 37679.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+50S ribosomal protein ... , 30 types, 30 molecules CDEFGHIJKLMNOPQRSTUVWXYZ123456
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Pseudomonas aeruginosa 70s ribosome from a clinical isolate Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 319022 / Symmetry type: POINT |