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Yorodumi- PDB-7kgf: Cryo-EM Structures of AdeB from Acinetobacter baumannii: AdeB-III -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kgf | ||||||
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Title | Cryo-EM Structures of AdeB from Acinetobacter baumannii: AdeB-III | ||||||
Components | Efflux pump membrane transporter | ||||||
Keywords | TRANSPORT PROTEIN / AdeB / Acinetobacter baumannii / Membrane Protein / Cryo-EM / RND transporter | ||||||
Function / homology | Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane / Efflux pump membrane transporter Function and homology information | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å | ||||||
Authors | Morgan, C.E. / Yu, E.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: mBio / Year: 2021 Title: Cryoelectron Microscopy Structures of AdeB Illuminate Mechanisms of Simultaneous Binding and Exporting of Substrates. Authors: Christopher E Morgan / Przemyslaw Glaza / Inga V Leus / Anhthu Trinh / Chih-Chia Su / Meng Cui / Helen I Zgurskaya / Edward W Yu / Abstract: is a Gram-negative pathogen that has emerged as one of the most highly antibiotic-resistant bacteria worldwide. Multidrug efflux within these highly drug-resistant strains and other opportunistic ... is a Gram-negative pathogen that has emerged as one of the most highly antibiotic-resistant bacteria worldwide. Multidrug efflux within these highly drug-resistant strains and other opportunistic pathogens is a major cause of failure of drug-based treatments of infectious diseases. The best-characterized multidrug efflux system in is the prevalent rug fflux B (AdeB) pump, which is a member of the resistance-nodulation-cell division (RND) superfamily. Here, we report six structures of the trimeric AdeB multidrug efflux pump in the presence of ethidium bromide using single-particle cryoelectron microscopy (cryo-EM). These structures allow us to directly observe various novel conformational states of the AdeB trimer, including the transmembrane region of trimeric AdeB can be associated with form a trimer assembly or dissociated into "dimer plus monomer" and "monomer plus monomer plus monomer" configurations. We also discover that a single AdeB protomer can simultaneously anchor a number of ethidium ligands and that different AdeB protomers can bind ethidium molecules simultaneously. Combined with molecular dynamics (MD) simulations, we reveal a drug transport mechanism that involves multiple multidrug-binding sites and various transient states of the AdeB membrane protein. Our data suggest that each AdeB protomer within the trimer binds and exports drugs independently. has emerged as one of the most highly antibiotic-resistant Gram-negative pathogens. The prevalent AdeB multidrug efflux pump mediates resistance to a broad spectrum of clinically relevant antimicrobial agents. Here, we report six cryo-EM structures of the trimeric AdeB pump in the presence of ethidium bromide. We discover that a single AdeB protomer can simultaneously anchor a number of ligands, and different AdeB protomers can bind ethidium molecules simultaneously. The results indicate that each AdeB protomer within the trimer recognizes and extrudes drugs independently. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7kgf.cif.gz | 505.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kgf.ent.gz | 416.6 KB | Display | PDB format |
PDBx/mmJSON format | 7kgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kgf_validation.pdf.gz | 894.3 KB | Display | wwPDB validaton report |
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Full document | 7kgf_full_validation.pdf.gz | 927.9 KB | Display | |
Data in XML | 7kgf_validation.xml.gz | 76.4 KB | Display | |
Data in CIF | 7kgf_validation.cif.gz | 116.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/7kgf ftp://data.pdbj.org/pub/pdb/validation_reports/kg/7kgf | HTTPS FTP |
-Related structure data
Related structure data | 22868MC 7kgdC 7kgeC 7kggC 7kghC 7kgiC 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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-Components
#1: Protein | Mass: 112588.297 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: adeB, acrB, 32_436, CBI29_01998, EA686_00900 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FD70 |
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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: AdeB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 |
Image recording | Electron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: cryoSPARC / Version: 2.15 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C3 (3 fold cyclic) |
3D reconstruction | Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25060 / Symmetry type: POINT |