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- EMDB-1552: Molecular Architecture of the 'stressosome', a signal transduction hub -

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Basic information

Entry
Database: EMDB / ID: EMD-1552
TitleMolecular Architecture of the 'stressosome', a signal transduction hub
Map dataRsbR146-274RsbS stressosome core with imposed icosahedral symmetry
Sample
  • Sample: RsbR146-274RsbS stressosome core
  • Protein or peptide: RsbR146-274RsbS
KeywordsRsbR / RsbS / Stressosome / sigmaB / RsbT / stress response / bacillus
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsMarles-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
CitationJournal: 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
DepositionSep 8, 2008-
Header (metadata) releaseSep 11, 2008-
Map releaseApr 16, 2009-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 30
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 30
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd1552.png

Downloads & links

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Map

FileDownload / File: emd_1552.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRsbR146-274RsbS stressosome core with imposed icosahedral symmetry
Voxel sizeX=Y=Z: 2.54 Å
Density
Contour Level1: 14.0 / Movie #1: 30
Minimum - Maximum-104.048000000000002 - 109.155000000000001
Average (Standard dev.)0.000000000238557 (±10.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-49-50
Dimensions100100100
Spacing100100100
CellA=B=C: 254 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.542.542.54
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z254.000254.000254.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS-49-50-50
NC/NR/NS100100100
D min/max/mean-104.048109.1550.000

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Supplemental data

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Sample components

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Entire : RsbR146-274RsbS stressosome core

EntireName: RsbR146-274RsbS stressosome core
Components
  • Sample: RsbR146-274RsbS stressosome core
  • Protein or peptide: RsbR146-274RsbS

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Supramolecule #1000: RsbR146-274RsbS stressosome core

SupramoleculeName: RsbR146-274RsbS stressosome core / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: RsbR146-274RsbS

MacromoleculeName: RsbR146-274RsbS / type: protein_or_peptide / ID: 1 / Name.synonym: Stressosome core / Recombinant expression: Yes
Source (natural)Organism: Bacillus subtilis (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: OTHER / Software - Name: IMAGIC

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Atomic model buiding 1

Initial modelPDB ID:

2vy9

DetailsHomology models for R and S were made from 2VY9 and fitted
RefinementSpace: REAL

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