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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: 1552
TitleMolecular Architecture of the 'stressosome', a signal transduction hub
KeywordsRsbR / RsbS / Stressosome / sigmaB / RsbT / stress response / bacillus
SampleRsbR146-274RsbS stressosome core
SourceBacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /
Map dataRsbR146-274RsbS stressosome core with imposed icosahedral symmetry
Methodsingle particle (icosahedral) reconstruction, at 6.5 A resolution
AuthorsMarles-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
CitationScience, 2008, 322, 92-96

Science, 2008, 322, 92-96 StrPapers
Molecular architecture of the "stressosome," a signal integration and transduction hub.
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

DateDeposition: Sep 8, 2008 / Header (metadata) release: Sep 11, 2008 / Map release: Apr 16, 2009 / Last update: Sep 8, 2008

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 30
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 30
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_1552.map.gz (map file in CCP4 format, 3908 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
2.54 A/pix
= 254. A
100 pix
2.54 A/pix
= 254. A
100 pix
2.54 A/pix
= 254. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.54 A
Density
Contour Level:14, 30 (movie #1):
Minimum - Maximum-104.048 - 109.155
Average (Standard dev.)2.38557e-10 (10)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin-50-49-50
Limit495049
Spacing100100100
CellA=B=C: 254 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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 / Number of components: 1

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Component #1: protein, RsbR146-274RsbS

ProteinName: RsbR146-274RsbS / a.k.a: Stressosome core / Recombinant expression: Yes
SourceSpecies: Bacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: NONE / Cryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
LensImaging mode: OTHER
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral)
3D reconstructionSoftware: IMAGIC / Resolution: 6.5 A / Resolution method: 1/2-bit

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Atomic model buiding

Modeling #1Refinement space: REAL
Details: Homology models for R and S were made from 2VY9 and fitted
Input PDB model: 2VY9

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