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Yorodumi- PDB-8a63: Cryo-EM structure of Listeria monocytogenes 50S ribosomal subunit. -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a63 | |||||||||
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Title | Cryo-EM structure of Listeria monocytogenes 50S ribosomal subunit. | |||||||||
Components |
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Keywords | RIBOSOME / Listeria monocytogenes / 50S | |||||||||
Function / homology | Function and homology information large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome ...large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Listeria monocytogenes EGD-e (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Koller, T.O. / Crowe-McAuliffe, C. / Wilson, D.N. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: Structural basis for HflXr-mediated antibiotic resistance in Listeria monocytogenes. Authors: Timm O Koller / Kathryn J Turnbull / Karolis Vaitkevicius / Caillan Crowe-McAuliffe / Mohammad Roghanian / Ondřej Bulvas / Jose A Nakamoto / Tatsuaki Kurata / Christina Julius / Gemma C ...Authors: Timm O Koller / Kathryn J Turnbull / Karolis Vaitkevicius / Caillan Crowe-McAuliffe / Mohammad Roghanian / Ondřej Bulvas / Jose A Nakamoto / Tatsuaki Kurata / Christina Julius / Gemma C Atkinson / Jörgen Johansson / Vasili Hauryliuk / Daniel N Wilson / Abstract: HflX is a ubiquitous bacterial GTPase that splits and recycles stressed ribosomes. In addition to HflX, Listeria monocytogenes contains a second HflX homolog, HflXr. Unlike HflX, HflXr confers ...HflX is a ubiquitous bacterial GTPase that splits and recycles stressed ribosomes. In addition to HflX, Listeria monocytogenes contains a second HflX homolog, HflXr. Unlike HflX, HflXr confers resistance to macrolide and lincosamide antibiotics by an experimentally unexplored mechanism. Here, we have determined cryo-EM structures of L. monocytogenes HflXr-50S and HflX-50S complexes as well as L. monocytogenes 70S ribosomes in the presence and absence of the lincosamide lincomycin. While the overall geometry of HflXr on the 50S subunit is similar to that of HflX, a loop within the N-terminal domain of HflXr, which is two amino acids longer than in HflX, reaches deeper into the peptidyltransferase center. Moreover, unlike HflX, the binding of HflXr induces conformational changes within adjacent rRNA nucleotides that would be incompatible with drug binding. These findings suggest that HflXr confers resistance using an allosteric ribosome protection mechanism, rather than by simply splitting and recycling antibiotic-stalled ribosomes. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a63.cif.gz | 2.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8a63.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 8a63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/8a63 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/8a63 | HTTPS FTP |
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-Related structure data
Related structure data | 15204MC 8a57C 8a5iC 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 ... , 27 types, 27 molecules 123456789GHIJKMNOPQRSTUVWXZ
-RNA chain , 2 types, 2 molecules AB
#10: RNA chain | Mass: 950710.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: GenBank: 523836572 |
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#11: RNA chain | Mass: 36716.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: GenBank: 1182963193 |
-Non-polymers , 5 types, 170 molecules
#30: Chemical | #31: Chemical | ChemComp-SPD / | #32: Chemical | ChemComp-MG / #33: Chemical | #34: Chemical | ChemComp-K / | |
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-Details
Has ligand of interest | N |
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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: Listeria monocytogenes 50S ribosomal subunit. / Type: RIBOSOME / Entity ID: #1-#29 / Source: NATURAL | |||||||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 1 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Listeria monocytogenes EGD-e (bacteria) | |||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: 0.05% Nikkol | |||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 5 OD260/mL | |||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / 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 / Nominal magnification: 165000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 30.255 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 110725 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14097 / Symmetry type: POINT |