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Yorodumi- EMDB-1558: Molecular Architecture of the 'stressosome', a signal transduction hub -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1558 | |||||||||
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Title | Molecular Architecture of the 'stressosome', a signal transduction hub | |||||||||
Map data | RsbR146-274RsbS Stressosome core with imposed D2 symmetry | |||||||||
Sample |
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Keywords | RsbR / RsbS / Stressosome / sigmaB / RsbT / stress response / bacillus | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.1 Å | |||||||||
Authors | Marles-Wright J / Grant T / Delumeau O / van Duinen G / Firbank SJ / Lewis PJ / Murray JW / Newman JA / Quin MB / Race PR ...Marles-Wright J / Grant T / Delumeau O / van Duinen G / Firbank SJ / Lewis PJ / Murray JW / Newman JA / Quin MB / Race PR / Rohou A / Tichelaar W / van Heel M / Lewis RJ | |||||||||
Citation | Journal: Science / Year: 2008 Title: Molecular architecture of the "stressosome," a signal integration and transduction hub. Authors: Jon Marles-Wright / Tim Grant / Olivier Delumeau / Gijs van Duinen / Susan J Firbank / Peter J Lewis / James W Murray / Joseph A Newman / Maureen B Quin / Paul R Race / Alexis Rohou / Willem ...Authors: Jon Marles-Wright / Tim Grant / Olivier Delumeau / Gijs van Duinen / Susan J Firbank / Peter J Lewis / James W Murray / Joseph A Newman / Maureen B Quin / Paul R Race / Alexis Rohou / Willem Tichelaar / Marin van Heel / Richard J Lewis / Abstract: A commonly used strategy by microorganisms to survive multiple stresses involves a signal transduction cascade that increases the expression of stress-responsive genes. Stress signals can be ...A commonly used strategy by microorganisms to survive multiple stresses involves a signal transduction cascade that increases the expression of stress-responsive genes. Stress signals can be integrated by a multiprotein signaling hub that responds to various signals to effect a single outcome. We obtained a medium-resolution cryo-electron microscopy reconstruction of the 1.8-megadalton "stressosome" from Bacillus subtilis. Fitting known crystal structures of components into this reconstruction gave a pseudoatomic structure, which had a virus capsid-like core with sensory extensions. We suggest that the different sensory extensions respond to different signals, whereas the conserved domains in the core integrate the varied signals. The architecture of the stressosome provides the potential for cooperativity, suggesting that the response could be tuned dependent on the magnitude of chemophysical insult. | |||||||||
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_1558.map.gz | 2.3 MB | EMDB map data format | |
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Header (meta data) | emd-1558-v30.xml emd-1558.xml | 7.9 KB 7.9 KB | Display Display | EMDB header |
Images | emd1558.png | 275.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1558 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1558 | HTTPS FTP |
-Validation report
Summary document | emd_1558_validation.pdf.gz | 243.3 KB | Display | EMDB validaton report |
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Full document | emd_1558_full_validation.pdf.gz | 242.4 KB | Display | |
Data in XML | emd_1558_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1558 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1558 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1558.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RsbR146-274RsbS Stressosome core with imposed D2 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.54 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 : RsbR146-274RsbS stressosome core
Entire | Name: RsbR146-274RsbS stressosome core |
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Components |
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-Supramolecule #1000: RsbR146-274RsbS stressosome core
Supramolecule | Name: RsbR146-274RsbS stressosome core / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: RsbR146-274RsbS Stressosome core
Macromolecule | Name: RsbR146-274RsbS Stressosome core / type: protein_or_peptide / ID: 1 / Name.synonym: Stressosome core / Recombinant expression: Yes |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: Vitrobot |
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-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Image recording | Digitization - Scanner: NIKON SUPER COOLSCAN 9000 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 13317 |
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-Atomic model buiding 1
Initial model | PDB ID: |
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Details | R and S were fitted using an homology model made using 2VY9 |
Refinement | Space: REAL |