+Open data
-Basic information
Entry | Database: PDB / ID: 9bft | ||||||
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Title | Cryo-EM co-structure of AcrB with CU244 | ||||||
Components | Multidrug efflux pump subunit AcrB | ||||||
Keywords | TRANSLOCASE / AcrB Multidrug Efflux Pump | ||||||
Function / homology | Function and homology information xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / outer membrane-bounded periplasmic space / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.44 Å | ||||||
Authors | Su, C.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: mBio / Year: 2023 Title: Bacterial efflux pump modulators prevent bacterial growth in macrophages and under broth conditions that mimic the host environment. Authors: Samual C Allgood / Chih-Chia Su / Amy L Crooks / Christian T Meyer / Bojun Zhou / Meredith D Betterton / Michael R Barbachyn / Edward W Yu / Corrella S Detweiler / Abstract: Bacterial efflux pumps are critical for resistance to antibiotics and for virulence. We previously identified small molecules that inhibit efflux pumps (efflux pump modulators, EPMs) and prevent ...Bacterial efflux pumps are critical for resistance to antibiotics and for virulence. We previously identified small molecules that inhibit efflux pumps (efflux pump modulators, EPMs) and prevent pathogen replication in host cells. Here, we used medicinal chemistry to increase the activity of the EPMs against pathogens in cells into the nanomolar range. We show by cryo-electron microscopy that these EPMs bind an efflux pump subunit. In broth culture, the EPMs increase the potency (activity), but not the efficacy (maximum effect), of antibiotics. We also found that bacterial exposure to the EPMs appear to enable the accumulation of a toxic metabolite that would otherwise be exported by efflux pumps. Thus, inhibitors of bacterial efflux pumps could interfere with infection not only by potentiating antibiotics, but also by allowing toxic waste products to accumulate within bacteria, providing an explanation for why efflux pumps are needed for virulence in the absence of antibiotics. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bft.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9bft.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9bft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bft_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 9bft_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 9bft_validation.xml.gz | 82.4 KB | Display | |
Data in CIF | 9bft_validation.cif.gz | 126.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/9bft ftp://data.pdbj.org/pub/pdb/validation_reports/bf/9bft | HTTPS FTP |
-Related structure data
Related structure data | 44506MC 9bfhC 9bfmC 9bfnC 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: 113665.180 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P31224 #2: Chemical | #3: Chemical | ChemComp-A1AOF / ( | Mass: 317.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18Cl2N2O2 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | 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: H6PD / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: This is from a heterogeneous and impure protein sample. |
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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 29 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162048 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
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