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Yorodumi- EMDB-1087: Three-dimensional structure of the bacterial multidrug transporte... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1087 | |||||||||
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Title | Three-dimensional structure of the bacterial multidrug transporter EmrE shows it is an asymmetric homodimer. | |||||||||
Map data | Density map of the asymmetric dimer of EmrE,a multidrug transporter from Escherichia coli | |||||||||
Sample |
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Function / homology | Function and homology information EmrE multidrug transporter complex / glycine betaine transport / amino-acid betaine transmembrane transporter activity / choline transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / antiporter activity / xenobiotic transport / response to osmotic stress / xenobiotic transmembrane transporter activity ...EmrE multidrug transporter complex / glycine betaine transport / amino-acid betaine transmembrane transporter activity / choline transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / antiporter activity / xenobiotic transport / response to osmotic stress / xenobiotic transmembrane transporter activity / transmembrane transporter activity / xenobiotic metabolic process / transmembrane transport / cellular response to xenobiotic stimulus / membrane => GO:0016020 / response to xenobiotic stimulus / DNA damage response / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | electron crystallography / cryo EM / negative staining / Resolution: 7.5 Å | |||||||||
Authors | Ubarretxena-Belandia I / Baldwin JM / Schuldiner S / Tate CG | |||||||||
Citation | Journal: EMBO J / Year: 2003 Title: Three-dimensional structure of the bacterial multidrug transporter EmrE shows it is an asymmetric homodimer. Authors: Iban Ubarretxena-Belandia / Joyce M Baldwin / Shimon Schuldiner / Christopher G Tate / Abstract: The small multidrug resistance family of transporters is widespread in bacteria and is responsible for bacterial resistance to toxic aromatic cations by proton-linked efflux. We have determined the ...The small multidrug resistance family of transporters is widespread in bacteria and is responsible for bacterial resistance to toxic aromatic cations by proton-linked efflux. We have determined the three-dimensional (3D) structure of the Escherichia coli multidrug transporter EmrE by electron cryomicroscopy of 2D crystals, including data to 7.0 A resolution. The structure of EmrE consists of a bundle of eight transmembrane alpha-helices with one substrate molecule bound near the centre. The substrate binding chamber is formed from six helices and is accessible both from the aqueous phase and laterally from the lipid bilayer. The most remarkable feature of the structure of EmrE is that it is an asymmetric homodimer. The possible arrangement of the two polypeptides in the EmrE dimer is discussed based on the 3D density map. | |||||||||
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_1087.map.gz | 547.4 KB | EMDB map data format | |
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Header (meta data) | emd-1087-v30.xml emd-1087.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
Images | 1087.gif | 11.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1087 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1087 | HTTPS FTP |
-Validation report
Summary document | emd_1087_validation.pdf.gz | 284.2 KB | Display | EMDB validaton report |
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Full document | emd_1087_full_validation.pdf.gz | 283.8 KB | Display | |
Data in XML | emd_1087_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1087 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1087 | HTTPS FTP |
-Related structure data
Related structure data | 2i68M M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1087.map.gz / Format: CCP4 / Size: 579.1 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Density map of the asymmetric dimer of EmrE,a multidrug transporter from Escherichia coli | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.48067 Å / Y: 0.57867 Å / Z: 2.5 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 : EmrE from E. coli containing the bound substrate tetraphenylphosp...
Entire | Name: EmrE from E. coli containing the bound substrate tetraphenylphosphonium |
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Components |
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-Supramolecule #1000: EmrE from E. coli containing the bound substrate tetraphenylphosp...
Supramolecule | Name: EmrE from E. coli containing the bound substrate tetraphenylphosphonium type: sample / ID: 1000 Details: EmrE in the 2D crystals is in a functional state with the substrate (TPP+) bound in a binding pocket formed from 6 out of the 8 helices in the asymmetric dimer. Oligomeric state: Asymmetric homodimer / Number unique components: 1 |
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Molecular weight | Theoretical: 15.2 KDa |
-Macromolecule #1: EmrE
Macromolecule | Name: EmrE / type: protein_or_peptide / ID: 1 / Name.synonym: MvrC, EB Details: 4-helix integral membrane protein; The engineered EmrE is fully functional as assessed by in vivo and in vitro transport assays Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K12 / Location in cell: Inner membrane |
Molecular weight | Experimental: 15.2 KDa / Theoretical: 15.2 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pT7-7 |
Sequence | UniProtKB: Multidrug transporter EmrE / GO: membrane => GO:0016020 / InterPro: Small drug/metabolite transporter protein family |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | electron crystallography |
Aggregation state | 2D array |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 Details: 20 mM Sodium phosphate pH7.5, 100 mM NaCl, 2mM MgCl2, 1mM EDTA, 1 mM Na azide, 10uM tetraphenylphosphonium |
Staining | Type: NEGATIVE Details: Crystals on carbon support were washed with 1% glucose pH 8 (aq ammonia) containing 25ug/ml bacitracin, 2 times 20ul, and blotted to dryness |
Grid | Details: 300 mesh molybdenum grid |
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 45 % / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: manual. Performed at room temperature Method: Blot to dryness for 10 seconds before freezing |
Details | 2D crystals were grown in suspension by dialysis |
Crystal formation | Details: 2D crystals were grown in suspension by dialysis |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Min: 77 K / Max: 77 K / Average: 77 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 200,000 times magnification |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 47 / Average electron dose: 15 e/Å2 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 57400 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 46 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 46 ° |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: OTHER / Software - Name: MRC Details: Resolution in the membrane plane is 7.5 angstroms and 16 angstroms perpendicular to the membrane plane |
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Crystal parameters | Unit cell - A: 72.1 Å / Unit cell - B: 86.8 Å / Unit cell - γ: 107.3 ° / Plane group: P 2 |
CTF correction | Details: CTFFIND2 on each image |