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Yorodumi- EMDB-22050: 3.9 Angstrom reconstruction of E.coli AcrB embedded in the liposome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22050 | |||||||||
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Title | 3.9 Angstrom reconstruction of E.coli AcrB embedded in the liposome | |||||||||
Map data | 3D reconstruction of AcrB after Density Modification | |||||||||
Sample |
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Function / homology | Function and homology information xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / outer membrane-bounded periplasmic space / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Xia Y / Fan X / Yan N | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Cryo-EM analysis of a membrane protein embedded in the liposome. Authors: Xia Yao / Xiao Fan / Nieng Yan / Abstract: Membrane proteins (MPs) used to be the most difficult targets for structural biology when X-ray crystallography was the mainstream approach. With the resolution revolution of single-particle electron ...Membrane proteins (MPs) used to be the most difficult targets for structural biology when X-ray crystallography was the mainstream approach. With the resolution revolution of single-particle electron cryo-microscopy (cryo-EM), rapid progress has been made for structural elucidation of isolated MPs. The next challenge is to preserve the electrochemical gradients and membrane curvature for a comprehensive structural elucidation of MPs that rely on these chemical and physical properties for their biological functions. Toward this goal, here we present a convenient workflow for cryo-EM structural analysis of MPs embedded in liposomes, using the well-characterized AcrB as a prototype. Combining optimized proteoliposome isolation, cryo-sample preparation on graphene grids, and an efficient particle selection strategy, the three-dimensional (3D) reconstruction of AcrB embedded in liposomes was obtained at 3.9 Å resolution. The conformation of the homotrimeric AcrB remains the same when the surrounding membranes display different curvatures. Our approach, which can be widely applied to cryo-EM analysis of MPs with distinctive soluble domains, lays out the foundation for cryo-EM analysis of integral or peripheral MPs whose functions are affected by transmembrane electrochemical gradients or/and membrane curvatures. | |||||||||
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_22050.map.gz | 6.7 MB | EMDB map data format | |
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Header (meta data) | emd-22050-v30.xml emd-22050.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22050_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_22050.png | 184.3 KB | ||
Others | emd_22050_additional_1.map.gz emd_22050_additional_2.map.gz | 28.1 MB 23 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22050 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22050 | HTTPS FTP |
-Related structure data
Similar structure data | |
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EM raw data | EMPIAR-10426 (Title: 3.9 Angstrom reconstruction of E.coli AcrB embedded in the liposome Data size: 9.6 TB Data #1: Unaligned multi-frame micrographs of AcrB embedded in the liposome. [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22050.map.gz / Format: CCP4 / Size: 7.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D reconstruction of AcrB after Density Modification | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.114 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: 3D reconstruction of AcrB after postprocess
File | emd_22050_additional_1.map | ||||||||||||
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Annotation | 3D reconstruction of AcrB after postprocess | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered 3D reconstruction of AcrB
File | emd_22050_additional_2.map | ||||||||||||
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Annotation | Unfiltered 3D reconstruction of AcrB | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : E.coli AcrB
Entire | Name: E.coli AcrB |
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Components |
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-Supramolecule #1: E.coli AcrB
Supramolecule | Name: E.coli AcrB / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 350 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Details: Ozonated |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal magnification: 105000 |
Specialist optics | Spherical aberration corrector: Cs corrector applied / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 4.0 µm / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 5757 / Average exposure time: 5.6 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |