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- PDB-6qcm: Cryo em structure of the Listeria stressosome -

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Basic information

Entry
Database: PDB / ID: 6qcm
TitleCryo em structure of the Listeria stressosome
Components
  • (RsbR protein) x 3
  • RsbR protein,RsbR protein
  • RsbS protein
KeywordsANTIMICROBIAL PROTEIN / Stressosome complex / stress response machine / Bacteria stress sensor
Function / homology
Function and homology information


oxygen binding / heme binding
Similarity search - Function
RsbS co-antagonist protein RsbRA N-terminal domain / Rsbr N terminal / : / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / Globin/Protoglobin
Similarity search - Domain/homology
RsbR protein / RsbS protein
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.21 Å
AuthorsWilliams, A.H. / Redzej, A. / Waksman, G. / Cossart, P.
Funding support United Kingdom, France, 2items
OrganizationGrant numberCountry
Wellcome Trust098302 United Kingdom
European Research Council670823 France
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 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / em_entity_assembly_molwt / pdbx_entry_details
Item: _em_admin.last_update

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Structure viewerMolecule:
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Assembly

Deposited unit
AB: RsbR protein
BC: RsbR protein
CB: RsbR protein
DB: RsbR protein
DC: RsbR protein
E: RsbR protein
EB: RsbR protein
F: RsbR protein
FA: RsbR protein
FB: RsbR protein
FC: RsbR protein
GB: RsbR protein
GC: RsbR protein
HC: RsbR protein
IB: RsbR protein
IC: RsbR protein
K: RsbR protein
KB: RsbR protein
L: RsbR protein
LB: RsbR protein
M: RsbR protein
OB: RsbR protein
P: RsbR protein
PB: RsbR protein
Q: RsbR protein
SB: RsbR protein
T: RsbR protein
TB: RsbR protein
U: RsbR protein
UB: RsbR protein
V: RsbR protein
VB: RsbR protein
W: RsbR protein
X: RsbR protein
Y: RsbR protein
Z: RsbR protein
A: RsbS protein
B: RsbS protein
C: RsbS protein
D: RsbS protein
I: RsbS protein
J: RsbS protein
N: RsbS protein
O: RsbS protein
R: RsbS protein
S: RsbS protein
a: RsbS protein
b: RsbS protein
c: RsbS protein
d: RsbS protein
e: RsbS protein
f: RsbS protein
g: RsbS protein
h: RsbS protein
i: RsbS protein
j: RsbS protein
AD: RsbR protein,RsbR protein
CD: RsbR protein
FD: RsbR protein
HD: RsbR protein


Theoretical massNumber of molelcules
Total (without water)812,97360
Polymers812,97360
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area120970 Å2
ΔGint-767 kcal/mol
Surface area320710 Å2
MethodPISA

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Components

#1: Protein ...
RsbR protein


Mass: 13944.500 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: RsbR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8Y8K9
#2: Protein
RsbR protein


Mass: 14073.681 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: RsbR / Plasmid: PGEX4T1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8Y8K9
#3: Protein
RsbS protein


Mass: 12606.707 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: rsbS / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q92DC5
#4: Protein RsbR protein,RsbR protein


Mass: 13479.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: RsbR / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Gold / References: UniProt: Q8Y8K9
#5: Protein RsbR protein


Mass: 14860.573 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: RsbR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8Y8K9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Listeria Stressosome CoreCOMPLEXThe subcomponents are, RsbR and RsbSall0MULTIPLE SOURCES
2RsbRORGANELLE OR CELLULAR COMPONENT#1-#2, #4-#51RECOMBINANT
3RsbSORGANELLE OR CELLULAR COMPONENT#31RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Listeria monocytogenes EGD-e (bacteria)169963
23Listeria monocytogenes EGD-e (bacteria)169963
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli BL21 (bacteria)511693
23Escherichia coli BL21 (bacteria)511693
Buffer solutionpH: 8.5
SpecimenConc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/PALLADIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 2.25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 20

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
1Gautomatchparticle selection
4CTFFIND4CTF correction
7Coot0.089model fitting
9PHENIX1.12model refinement
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 200000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78000 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00652978
ELECTRON MICROSCOPYf_angle_d1.17171708
ELECTRON MICROSCOPYf_dihedral_angle_d5.93433128
ELECTRON MICROSCOPYf_chiral_restr0.0699469
ELECTRON MICROSCOPYf_plane_restr0.0088901

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