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Yorodumi- EMDB-3398: Electron Cryotomography and subvolume averaging of the cytoplasmi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3398 | |||||||||
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Title | Electron Cryotomography and subvolume averaging of the cytoplasmic chemoreceptor array in Vibrio cholerae | |||||||||
Map data | subvolume average of the cytoplasmic array in V. cholerae | |||||||||
Sample |
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Keywords | chemotaxis / chemoreceptor / Vibrio cholerae / cytoplasmic chemoreceptor array | |||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM | |||||||||
Authors | Briegel A / Ortega D R / Mann P / Kjaer A / Ringgaard S / Jensen G J | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2016 Title: Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholerae and are stabilized by a double signaling domain receptor DosM. Authors: Ariane Briegel / Davi R Ortega / Petra Mann / Andreas Kjær / Simon Ringgaard / Grant J Jensen / Abstract: Nearly all motile bacterial cells use a highly sensitive and adaptable sensory system to detect changes in nutrient concentrations in the environment and guide their movements toward attractants and ...Nearly all motile bacterial cells use a highly sensitive and adaptable sensory system to detect changes in nutrient concentrations in the environment and guide their movements toward attractants and away from repellents. The best-studied bacterial chemoreceptor arrays are membrane-bound. Many motile bacteria contain one or more additional, sometimes purely cytoplasmic, chemoreceptor systems. Vibrio cholerae contains three chemotaxis clusters (I, II, and III). Here, using electron cryotomography, we explore V. cholerae's cytoplasmic chemoreceptor array and establish that it is formed by proteins from cluster I. We further identify a chemoreceptor with an unusual domain architecture, DosM, which is essential for formation of the cytoplasmic arrays. DosM contains two signaling domains and spans the two-layered cytoplasmic arrays. Finally, we present evidence suggesting that this type of receptor is important for the structural stability of the cytoplasmic array. | |||||||||
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_3398.map.gz | 1.9 MB | EMDB map data format | |
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Header (meta data) | emd-3398-v30.xml emd-3398.xml | 7.9 KB 7.9 KB | Display Display | EMDB header |
Images | DosMmap.tif | 226.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3398 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3398 | HTTPS FTP |
-Validation report
Summary document | emd_3398_validation.pdf.gz | 257.8 KB | Display | EMDB validaton report |
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Full document | emd_3398_full_validation.pdf.gz | 256.9 KB | Display | |
Data in XML | emd_3398_validation.xml.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3398 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3398 | 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_3398.map.gz / Format: CCP4 / Size: 2.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | subvolume average of the cytoplasmic array in V. cholerae | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.618 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 : cytoplasmic array subvolume average from whole cell tomogram
Entire | Name: cytoplasmic array subvolume average from whole cell tomogram |
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Components |
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-Supramolecule #1000: cytoplasmic array subvolume average from whole cell tomogram
Supramolecule | Name: cytoplasmic array subvolume average from whole cell tomogram type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: DosM
Macromolecule | Name: DosM / type: protein_or_peptide / ID: 1 / Oligomeric state: Dimer / Recombinant expression: No |
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Source (natural) | Organism: Vibrio cholerae (bacteria) / Location in cell: cytoplasm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Grid | Details: Quantifoil R2/2 copper grids, glow discharged |
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Vitrification | Cryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Jun 4, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 121 / Average electron dose: 160 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal magnification: 33000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Software - Name: imod / Number subtomograms used: 80 |
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CTF correction | Details: imod |