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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4508 | |||||||||
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Title | Cryo em structure of the Listeria stressosome | |||||||||
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![]() | Stressosome complex / stress response machine / Bacteria stress sensor / ANTIMICROBIAL PROTEIN | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.21 Å | |||||||||
![]() | Williams AH / Redzej A | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 21.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.8 KB 17.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.6 KB | Display | ![]() |
Images | ![]() | 83.1 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 251 KB | Display | ![]() |
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Full document | ![]() | 250.1 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qcmMC ![]() 4510C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size |
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Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Listeria Stressosome Core
Entire | Name: Listeria Stressosome Core |
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Components |
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-Supramolecule #1: Listeria Stressosome Core
Supramolecule | Name: Listeria Stressosome Core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: The subcomponents are, RsbR and RsbS |
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Molecular weight | Theoretical: 1.8 MDa |
-Supramolecule #2: RsbR
Supramolecule | Name: RsbR / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #4-#5 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: RsbS
Supramolecule | Name: RsbS / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: RsbR protein
Macromolecule | Name: RsbR protein / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.9445 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SALQELSAPL LPIFEKISVM PLIGTIDTER AKLIIENLLI GVVKNRSEVV LIDITGVPVV DTMVAHHIIQ ASEAVRLVGC QAMLVGIRP EIAQTIVNLG IELDQIITTN TMKKGMERAL ALTNREIVE UniProtKB: RsbR protein |
-Macromolecule #2: RsbR protein
Macromolecule | Name: RsbR protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.073681 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: KSALQELSAP LLPIFEKISV MPLIGTIDTE RAKLIIENLL IGVVKNRSEV VLIDITGVPV VDTMVAHHII QASEAVRLVG CQAMLVGIR PEIAQTIVNL GIELDQIITT NTMKKGMERA LALTNREIVE UniProtKB: RsbR protein |
-Macromolecule #3: RsbS protein
Macromolecule | Name: RsbS protein / type: protein_or_peptide / ID: 3 / Number of copies: 20 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.606707 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGIPILKLGE CLLISIQSEL DDHTAVEFQE DLLAKIHETS ARGVVIDITS IDFIDSFIAK ILGDVVSMSK LMGAKVVVTG IQPAVAITL IELGITFSGV LSAMDLESGL EKLKQELGE UniProtKB: RsbS protein |
-Macromolecule #4: RsbR protein,RsbR protein
Macromolecule | Name: RsbR protein,RsbR protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.479988 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: EKTVSIQKSA LQELSAPLLP IFEKISVMPL IGTIDTERAK LIIENLLIGV VKNRSEVVLI DITGVPVVDT MVAHHIIQAS EAVRLVGCQ AMLVGIRPEQ IITTNTMKKG MERALALTNR EIVE UniProtKB: RsbR protein, RsbR protein |
-Macromolecule #5: RsbR protein
Macromolecule | Name: RsbR protein / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.860573 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: EKTVSIQKSA LQELSAPLLP IFEKISVMPL IGTIDTERAK LIIENLLIGV VKNRSEVVLI DITGVPVVDT MVAHHIIQAS EAVRLVGCQ AMLVGIRPEI AQTIVNLGIE LDQIITTNTM KKGMERALAL TNREIVE UniProtKB: RsbR protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 8.5 |
Grid | Model: Quantifoil R2/2 / Material: COPPER/PALLADIUM / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 10.0 sec. / Average electron dose: 2.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | ![]() PDB-6qcm: |