+Open data
-Basic information
Entry | Database: PDB / ID: 6spg | |||||||||||||||
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Title | Pseudomonas aeruginosa 70s ribosome from a clinical isolate | |||||||||||||||
Components |
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Keywords | RIBOSOME / Pseudomonas aeruginosa | |||||||||||||||
Function / homology | Function and homology information large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å | |||||||||||||||
Authors | 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 | Denmark, 4items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6spg.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6spg.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6spg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/6spg ftp://data.pdbj.org/pub/pdb/validation_reports/sp/6spg | HTTPS FTP |
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-Related structure data
Related structure data | 10285MC 6spbC 6spcC 6spdC 6speC 6spfC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules aAB
#1: RNA chain | Mass: 494643.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: GenBank: 1353913695 |
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#22: RNA chain | Mass: 935990.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: REF: 470469287 |
#23: RNA chain | Mass: 37679.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: GenBank: 1384417243 |
-30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu
#2: Protein | Mass: 26684.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A072ZPV8 |
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#3: Protein | Mass: 23438.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A140S919 |
#4: Protein | Mass: 23187.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A072ZDF7 |
#5: Protein | Mass: 16432.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A241XG65 |
#6: Protein | Mass: 12278.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A069Q263 |
#7: Protein | Mass: 17313.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A2V3F2U6 |
#8: Protein | Mass: 14059.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXT9 |
#9: Protein | Mass: 14139.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A069PXX1 |
#10: Protein | Mass: 10886.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXT0 |
#11: Protein | Mass: 12086.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXU4 |
#12: Protein | Mass: 13569.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A071L394 |
#13: Protein | Mass: 12307.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXU3 |
#14: Protein | Mass: 11203.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXT8 |
#15: Protein | Mass: 9776.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A071L3R7 |
#16: Protein | Mass: 8762.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A2V4FRZ2 |
#17: Protein | Mass: 8848.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXT5 |
#18: Protein | Mass: 8346.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A2V3DLV3 |
#19: Protein | Mass: 9182.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: E2RXT2 |
#20: Protein | Mass: 9426.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A072ZDZ9 |
#21: Protein | Mass: 7519.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A069QC99 |
+50S ribosomal protein ... , 29 types, 29 molecules CDEFGHIJKLMNOPQRSTUVWXZ123456
-Protein / Non-polymers , 2 types, 173 molecules Y
#46: Protein | Mass: 6807.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) |
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#54: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Pseudomonas aeruginosa 70s ribosome from a clinical isolate Type: RIBOSOME / Entity ID: #1-#53 / Source: NATURAL |
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Source (natural) | Organism: Pseudomonas aeruginos (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||
3D reconstruction | Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128795 / Symmetry type: POINT |