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Yorodumi- PDB-8p1i: Single particle cryo-EM co-structure of Klebsiella pneumoniae Acr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p1i | |||||||||
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Title | Single particle cryo-EM co-structure of Klebsiella pneumoniae AcrB with the BDM91288 efflux pump inhibitor at 2.97 Angstrom resolution | |||||||||
Components | Efflux pump membrane transporter | |||||||||
Keywords | TRANSPORT PROTEIN / Efflux Pump Inhibitor / Transmembrane Binding / Antibiotic Resistance | |||||||||
Function / homology | Chem-PG8 / 3-chloranyl-2,6-di(piperazin-4-ium-1-yl)quinoline / Chem-WR6 / : Function and homology information | |||||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
Authors | Boernsen, C. / Mueller, R.T. / Pos, K.M. / Frangakis, A.S. | |||||||||
Funding support | Germany, France, 2items
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Citation | Journal: EMBO Mol Med / Year: 2024 Title: Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against K. pneumoniae. Authors: Anais Vieira Da Cruz / Juan-Carlos Jiménez-Castellanos / Clara Börnsen / Laurye Van Maele / Nina Compagne / Elizabeth Pradel / Reinke T Müller / Virginie Meurillon / Daphnée Soulard / ...Authors: Anais Vieira Da Cruz / Juan-Carlos Jiménez-Castellanos / Clara Börnsen / Laurye Van Maele / Nina Compagne / Elizabeth Pradel / Reinke T Müller / Virginie Meurillon / Daphnée Soulard / Catherine Piveteau / Alexandre Biela / Julie Dumont / Florence Leroux / Benoit Deprez / Nicolas Willand / Klaas M Pos / Achilleas S Frangakis / Ruben C Hartkoorn / Marion Flipo / Abstract: Antimicrobial resistance is a global problem, rendering conventional treatments less effective and requiring innovative strategies to combat this growing threat. The tripartite AcrAB-TolC efflux pump ...Antimicrobial resistance is a global problem, rendering conventional treatments less effective and requiring innovative strategies to combat this growing threat. The tripartite AcrAB-TolC efflux pump is the dominant constitutive system by which Enterobacterales like Escherichia coli and Klebsiella pneumoniae extrude antibiotics. Here, we describe the medicinal chemistry development and drug-like properties of BDM91288, a pyridylpiperazine-based AcrB efflux pump inhibitor. In vitro evaluation of BDM91288 confirmed it to potentiate the activity of a panel of antibiotics against K. pneumoniae as well as revert clinically relevant antibiotic resistance mediated by acrAB-tolC overexpression. Using cryo-EM, BDM91288 binding to the transmembrane region of K. pneumoniae AcrB was confirmed, further validating the mechanism of action of this inhibitor. Finally, proof of concept studies demonstrated that oral administration of BDM91288 significantly potentiated the in vivo efficacy of levofloxacin treatment in a murine model of K. pneumoniae lung infection. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p1i.cif.gz | 972.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p1i.ent.gz | 814 KB | Display | PDB format |
PDBx/mmJSON format | 8p1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/8p1i ftp://data.pdbj.org/pub/pdb/validation_reports/p1/8p1i | HTTPS FTP |
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-Related structure data
Related structure data | 17350MC 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
#1: Protein | Mass: 114489.945 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940 (bacteria) Strain: FDAARGOS_775 / Gene: UUU_08720 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C43(DE3)deltaacrAB / References: UniProt: J2LW81 #2: Chemical | ChemComp-WQW / | #3: Chemical | ChemComp-WR6 / [( | #4: Chemical | 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: Trimeric Klebsiella pneumoniae AcrB with BDM91288 efflux pump inhibitor Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940 (bacteria) Strain: FDAARGOS_775 | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C43(DE3)deltaacrAB | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: 130000 X / Calibrated magnification: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8487 |
EM imaging optics | Energyfilter name: GIF Quantum SE / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Particle selection | Num. of particles selected: 380181 | ||||||||||||
3D reconstruction | Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168689 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |