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- EMDB-4510: Cryo em structure of the Listeria stressosome -

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Basic information

Entry
Database: EMDB / ID: EMD-4510
TitleCryo em structure of the Listeria stressosome
Map data
Sample
  • Complex: Listeria Stressosome
    • Protein or peptide: RsbR
Biological speciesListeria monocytogenes (bacteria) / Listeria monocytogenes EGD-E (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsWilliams AH / Redzej A
CitationJournal: Nat Commun / Year: 2019
Title: The cryo-electron microscopy supramolecular structure of the bacterial stressosome unveils its mechanism of activation.
Authors: Allison H Williams / Adam Redzej / Nathalie Rolhion / Tiago R D Costa / Aline Rifflet / Gabriel Waksman / Pascale Cossart /
Abstract: How the stressosome, the epicenter of the stress response in bacteria, transmits stress signals from the environment has remained elusive. The stressosome consists of multiple copies of three ...How the stressosome, the epicenter of the stress response in bacteria, transmits stress signals from the environment has remained elusive. The stressosome consists of multiple copies of three proteins RsbR, RsbS and RsbT, a kinase that is important for its activation. Using cryo-electron microscopy, we determined the atomic organization of the Listeria monocytogenes stressosome at 3.38 Å resolution. RsbR and RsbS are organized in a 60-protomers truncated icosahedron. A key phosphorylation site on RsbR (T209) is partially hidden by an RsbR flexible loop, whose "open" or "closed" position could modulate stressosome activity. Interaction between three glutamic acids in the N-terminal domain of RsbR and the membrane-bound mini-protein Prli42 is essential for Listeria survival to stress. Together, our data provide the atomic model of the stressosome core and highlight a loop important for stressosome activation, paving the way towards elucidating the mechanism of signal transduction by the stressosome in bacteria.
History
DepositionDec 30, 2018-
SupersessionSep 11, 2019ID: EMD-4509
Header (metadata) releaseSep 11, 2019-
Map releaseSep 11, 2019-
UpdateSep 11, 2019-
Current statusSep 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4510.png

Downloads & links

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Map

FileDownload / File: emd_4510.map.gz / Format: CCP4 / Size: 262.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
410 Å/pix.
x 410 pix.
= 168100. Å		410 Å/pix.
x 410 pix.
= 168100. Å		410 Å/pix.
x 410 pix.
= 168100. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.410410410
CCP4 map header410410410
EM Navigator Movie #11.061.061.06
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.10136106 - 0.20301498
Average (Standard dev.)0.00033036378 (±0.0052886796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions410410410
Spacing410410410
CellA=B=C: 168100.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z410410410
M x/y/z410410410
origin x/y/z0.0000.0000.000
length x/y/z168100.000168100.000168100.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS410410410
D min/max/mean-0.1010.2030.000

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Supplemental data

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Sample components

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Entire : Listeria Stressosome

EntireName: Listeria Stressosome
Components
  • Complex: Listeria Stressosome
    • Protein or peptide: RsbR

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Supramolecule #1: Listeria Stressosome

SupramoleculeName: Listeria Stressosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: The subcomponents are, RsbR, RsbR and he RsbT.
Source (natural)Organism: Listeria monocytogenes (bacteria) / Strain: EGD-e
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: Bl21
Molecular weightExperimental: 1.8 MDa

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Macromolecule #1: RsbR

MacromoleculeName: RsbR / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Listeria monocytogenes EGD-E (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYKDFANFIR TNKADLLNDW MNEMEKQSDQ LINDIAKEAM YEETSKEFVD LIVSNVTENG SKFNEKLDDF AEKVVHLGW PIHFVTTGLR VFGLLVYTAM RDEDLFLKRE EKPEDDAYYR FETWLSSMYN KVVTAYADTW E KTVSIQKS ALQELSAPLL PIFEKISVMP ...String:
MYKDFANFIR TNKADLLNDW MNEMEKQSDQ LINDIAKEAM YEETSKEFVD LIVSNVTENG SKFNEKLDDF AEKVVHLGW PIHFVTTGLR VFGLLVYTAM RDEDLFLKRE EKPEDDAYYR FETWLSSMYN KVVTAYADTW E KTVSIQKS ALQELSAPLL PIFEKISVMP LIGTIDTERA KLIIENLLIG VVKNRSEVVL IDITGVPVVD TM VAHHIIQ ASEAVRLVGC QAMLVGIRPE IAQTIVNLGI ELDQIITTNT MKKGMERALA LTNREIVEKE G

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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

Concentration0.02 mg/mL
BufferpH: 8.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 10.0 sec. / Average electron dose: 2.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 100000
CTF correctionSoftware - Name: CTFFIND
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 78000
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

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