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Yorodumi- EMDB-1972: Complex of E. coli MacA-AcrA hybrid and Aa MacA-TolC hybrid dimer -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1972 | |||||||||
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Title | Complex of E. coli MacA-AcrA hybrid and Aa MacA-TolC hybrid dimer | |||||||||
Map data | This is an image of a surface rendered side-view of TolC and AcrA complex | |||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / Resolution: 37.0 Å | |||||||||
Authors | Xu Y / Lee M / Moeller A / Song S / Yoon BY / Kim HM / Jun SY / Lee K / Ha NC | |||||||||
Citation | Journal: J Biol Chem / Year: 2011 Title: Funnel-like hexameric assembly of the periplasmic adapter protein in the tripartite multidrug efflux pump in gram-negative bacteria. Authors: Yongbin Xu / Minho Lee / Arne Moeller / Saemee Song / Bo-Young Yoon / Hong-Man Kim / So-Young Jun / Kangseok Lee / Nam-Chul Ha / Abstract: Gram-negative bacteria expel diverse toxic chemicals through the tripartite efflux pumps spanning both the inner and outer membranes. The Escherichia coli AcrAB-TolC pump is the principal multidrug ...Gram-negative bacteria expel diverse toxic chemicals through the tripartite efflux pumps spanning both the inner and outer membranes. The Escherichia coli AcrAB-TolC pump is the principal multidrug exporter that confers intrinsic drug tolerance to the bacteria. The inner membrane transporter AcrB requires the outer membrane factor TolC and the periplasmic adapter protein AcrA. However, it remains ambiguous how the three proteins are assembled. In this study, a hexameric model of the adapter protein was generated based on the propensity for trimerization of a dimeric unit, and this model was further validated by presenting its channel-forming property that determines the substrate specificity. Genetic, in vitro complementation, and electron microscopic studies provided evidence for the binding of the hexameric adapter protein to the outer membrane factor in an intermeshing cogwheel manner. Structural analyses suggested that the adapter covers the periplasmic region of the inner membrane transporter. Taken together, we propose an adapter bridging model for the assembly of the tripartite pump, where the adapter protein provides a bridging channel and induces the channel opening of the outer membrane factor in the intermeshing tip-to-tip manner. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1972.map.gz | 4.9 MB | EMDB map data format | |
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Header (meta data) | emd-1972-v30.xml emd-1972.xml | 8 KB 8 KB | Display Display | EMDB header |
Images | EMD-1972.png | 45 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1972 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1972 | HTTPS FTP |
-Validation report
Summary document | emd_1972_validation.pdf.gz | 186.1 KB | Display | EMDB validaton report |
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Full document | emd_1972_full_validation.pdf.gz | 185.2 KB | Display | |
Data in XML | emd_1972_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1972 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1972 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1972.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is an image of a surface rendered side-view of TolC and AcrA complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.48 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : E. coli MacA-AcrA Hybrid and Aa MacATolC Hybrid Dimer
Entire | Name: E. coli MacA-AcrA Hybrid and Aa MacATolC Hybrid Dimer |
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Components |
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-Supramolecule #1000: E. coli MacA-AcrA Hybrid and Aa MacATolC Hybrid Dimer
Supramolecule | Name: E. coli MacA-AcrA Hybrid and Aa MacATolC Hybrid Dimer / type: sample / ID: 1000 / Number unique components: 2 |
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-Macromolecule #1: MacA-AcrA Hybrid
Macromolecule | Name: MacA-AcrA Hybrid / type: protein_or_peptide / ID: 1 / Name.synonym: AcrA / Oligomeric state: hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #2: Aa MacATolC Hybrid Dimer
Macromolecule | Name: Aa MacATolC Hybrid Dimer / type: protein_or_peptide / ID: 2 / Name.synonym: TolC / Oligomeric state: hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Oct 11, 2010 |
Image recording | Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder: room temperature / Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: whole image |
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Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC-5 APPION |