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Yorodumi- PDB-7ttu: 50S ribosomal subunit from Staphylococcus aureus (Strain ATCC43300) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ttu | ||||||||||||
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Title | 50S ribosomal subunit from Staphylococcus aureus (Strain ATCC43300) | ||||||||||||
Components |
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Keywords | RIBOSOME / 50S subunit / antibiotic resistance | ||||||||||||
Function / homology | Function and homology information 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 / translation / ribonucleoprotein complex / mRNA binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||||||||
Authors | Belousoff, M.J. / Piper, S. / Johnson, R. | ||||||||||||
Funding support | United States, Australia, 3items
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Citation | Journal: Microbiol Spectr / Year: 2022 Title: A Structurally Characterized Evolutionary Escape Route from Treatment with the Antibiotic Linezolid. Authors: Laura Perlaza-Jiménez / Kher-Shing Tan / Sarah J Piper / Rachel M Johnson / Rebecca S Bamert / Christopher J Stubenrauch / Alexander Wright / David Lupton / Trevor Lithgow / Matthew J Belousoff / Abstract: Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen that presents great health concerns. Treatment requires the use of last-line antibiotics, such as members of the ...Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen that presents great health concerns. Treatment requires the use of last-line antibiotics, such as members of the oxazolidinone family, of which linezolid is the first member to see regular use in the clinic. Here, we report a short time scale selection experiment in which strains of MRSA were subjected to linezolid treatment. Clonal isolates which had evolved a linezolid-resistant phenotype were characterized by whole-genome sequencing. Linezolid-resistant mutants were identified which had accumulated mutations in the ribosomal protein uL3. Multiple clones which had two mutations in uL3 exhibited resistance to linezolid, 2-fold higher than the clinical breakpoint. Ribosomes from this strain were isolated and subjected to single-particle cryo-electron microscopic analysis and compared to the ribosomes from the parent strain. We found that the mutations in uL3 lead to a rearrangement of a loop that makes contact with Helix 90, propagating a structural change over 15 Å away. This distal change swings nucleotide U2504 into the binding site of the antibiotic, causing linezolid resistance. Antibiotic resistance poses a critical problem to human health and decreases the utility of these lifesaving drugs. Of particular concern is the "superbug" methicillin-resistant Staphylococcus aureus (MRSA), for which treatment of infection requires the use of last-line antibiotics, including linezolid. In this paper, we characterize the atomic rearrangements which the ribosome, the target of linezolid, undergoes during its evolutionary journey toward becoming drug resistant. Using cryo-electron microscopy, we describe a particular molecular mechanism which MRSA uses to become resistant to linezolid. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ttu.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ttu.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 7ttu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ttu_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7ttu_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7ttu_validation.xml.gz | 125.1 KB | Display | |
Data in CIF | 7ttu_validation.cif.gz | 211 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/7ttu ftp://data.pdbj.org/pub/pdb/validation_reports/tt/7ttu | HTTPS FTP |
-Related structure data
Related structure data | 26124MC 7ttwC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+50S ribosomal protein ... , 25 types, 25 molecules ABCDEFGHIJKLMNOPQRSVWXYZa
-RNA chain , 2 types, 2 molecules 12
#26: RNA chain | Mass: 946680.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1877770729 |
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#27: RNA chain | Mass: 36998.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) |
-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: 50S ribosomal subunit from Staphylococcus aureus / Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 47.5 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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