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- EMDB-1556: Molecular Architecture of the 'stressosome', a signal transduction hub -

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Basic information

Entry
Database: EMDB / ID: EMD-1556
TitleMolecular Architecture of the 'stressosome', a signal transduction hub
Map dataTernary RsbR RsbS RsbT complex
Sample
  • Sample: Ternary RsbR RsbS RsbT complex
  • Protein or peptide: Ternary RsbR RsbS RsbT 'stressosome' complex
KeywordsRsbR / RsbS / Stressosome / sigmaB / RsbT / stress response / bacillus
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 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-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 24
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 24
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd1556.png

Downloads & links

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Map

FileDownload / File: emd_1556.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTernary RsbR RsbS RsbT complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 144 pix.
= 403.2 Å		2.8 Å/pix.
x 144 pix.
= 403.2 Å		2.8 Å/pix.
x 144 pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 14.0 / Movie #1: 24
Minimum - Maximum-86.6691 - 145.227000000000004
Average (Standard dev.)-0.00000000090205 (±10.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-71-72
Dimensions144144144
Spacing144144144
CellA=B=C: 403.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z403.200403.200403.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS-71-72-72
NC/NR/NS144144144
D min/max/mean-86.669145.227-0.000

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Supplemental data

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Sample components

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Entire : Ternary RsbR RsbS RsbT complex

EntireName: Ternary RsbR RsbS RsbT complex
Components
  • Sample: Ternary RsbR RsbS RsbT complex
  • Protein or peptide: Ternary RsbR RsbS RsbT 'stressosome' complex

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Supramolecule #1000: Ternary RsbR RsbS RsbT complex

SupramoleculeName: Ternary RsbR RsbS RsbT complex / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: Ternary RsbR RsbS RsbT 'stressosome' complex

MacromoleculeName: Ternary RsbR RsbS RsbT 'stressosome' complex / type: protein_or_peptide / ID: 1 / Name.synonym: Stressosome RsbT complex / 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 / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/HE
Image recordingDigitization - Scanner: NIKON SUPER COOLSCAN 9000
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: CM300 Stage / Specimen holder model: OTHER

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Image processing

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: OTHER / Software - Name: IMAGIC

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Atomic model buiding 1

Initial model(PDB ID:

2bnl

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2vy9

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1th8

)
DetailsA homology model for RsbT was constructed using 1TH8
RefinementSpace: REAL

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