[English] 日本語
Yorodumi
- PDB-7b0u: Stressosome complex from Listeria innocua -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7b0u
TitleStressosome complex from Listeria innocua
Components
  • (RsbR protein) x 4
  • RsbS protein
KeywordsSIGNALING PROTEIN / Stressosome / stress sensing / general stress response / phosphorylation cascade
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
RsbS protein / RsbR protein
Similarity search - Component
Biological speciesListeria innocua serovar 6a
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsMiksys, A. / Fu, L. / Madej, M.G. / Ziegler, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission721456 Germany
CitationJournal: Commun Biol / Year: 2022
Title: Molecular insights into intra-complex signal transmission during stressosome activation.
Authors: Algirdas Miksys / Lifei Fu / M Gregor Madej / Duarte N Guerreiro / Susann Kaltwasser / Maria Conway / Sema Ejder / Astrid Bruckmann / Jon Marles-Wright / Richard J Lewis / Conor O'Byrne / ...Authors: Algirdas Miksys / Lifei Fu / M Gregor Madej / Duarte N Guerreiro / Susann Kaltwasser / Maria Conway / Sema Ejder / Astrid Bruckmann / Jon Marles-Wright / Richard J Lewis / Conor O'Byrne / Jan Pané-Farré / Christine Ziegler /
Abstract: The stressosome is a pseudo-icosahedral megadalton bacterial stress-sensing protein complex consisting of several copies of two STAS-domain proteins, RsbR and RsbS, and the kinase RsbT. Upon ...The stressosome is a pseudo-icosahedral megadalton bacterial stress-sensing protein complex consisting of several copies of two STAS-domain proteins, RsbR and RsbS, and the kinase RsbT. Upon perception of environmental stress multiple copies of RsbT are released from the surface of the stressosome. Free RsbT activates downstream proteins to elicit a global cellular response, such as the activation of the general stress response in Gram-positive bacteria. The molecular events triggering RsbT release from the stressosome surface remain poorly understood. Here we present the map of Listeria innocua RsbR1/RsbS complex at resolutions of 3.45 Å for the STAS domain core in icosahedral symmetry and of 3.87 Å for the STAS domain and N-terminal sensors in D2 symmetry, respectively. The structure reveals a conformational change in the STAS domain linked to phosphorylation in RsbR. Docking studies indicate that allosteric RsbT binding to the conformationally flexible N-terminal sensor domain of RsbR affects the affinity of RsbS towards RsbT. Our results bring to focus the molecular events within the stressosome complex and further our understanding of this ubiquitous signaling hub.
History
DepositionNov 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-11971
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11971
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RsbR protein
B: RsbR protein
C: RsbR protein
D: RsbR protein
E: RsbS protein
F: RsbS protein
G: RsbR protein
H: RsbR protein
I: RsbS protein
J: RsbR protein
M: RsbR protein
N: RsbS protein
O: RsbS protein
P: RsbR protein
Q: RsbR protein
K: RsbR protein
L: RsbR protein
R: RsbR protein
S: RsbR protein
T: RsbS protein
U: RsbS protein
V: RsbR protein
W: RsbR protein
X: RsbS protein
Y: RsbR protein
Z: RsbR protein
a: RsbS protein
b: RsbS protein
c: RsbR protein
d: RsbR protein
e: RsbR protein
f: RsbR protein
g: RsbR protein
h: RsbR protein
i: RsbS protein
j: RsbS protein
k: RsbR protein
l: RsbR protein
m: RsbS protein
n: RsbR protein
o: RsbR protein
p: RsbS protein
q: RsbS protein
r: RsbR protein
s: RsbR protein
t: RsbR protein
u: RsbR protein
v: RsbR protein
w: RsbR protein
x: RsbS protein
y: RsbS protein
z: RsbR protein
0: RsbR protein
1: RsbS protein
2: RsbR protein
3: RsbR protein
4: RsbS protein
5: RsbS protein
6: RsbR protein
7: RsbR protein


Theoretical massNumber of molelcules
Total (without water)1,522,55760
Polymers1,522,55760
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area173600 Å2
ΔGint-1342 kcal/mol
Surface area608290 Å2
MethodPISA

-
Components

#1: Protein
RsbR protein


Mass: 31704.586 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)
Strain: ATCC BAA-680 / CLIP 11262 / Gene: RsbR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q92DC6
#2: Protein
RsbR protein


Mass: 31784.566 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)
Strain: ATCC BAA-680 / CLIP 11262 / Gene: RsbR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q92DC6
#3: Protein
RsbS protein


Mass: 12606.707 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)
Strain: ATCC BAA-680 / CLIP 11262 / Gene: rsbS / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q7AP18
#4: Protein
RsbR protein


Mass: 31864.547 Da / Num. of mol.: 4 / Mutation: T175/241-TPO
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)
Strain: ATCC BAA-680 / CLIP 11262 / Gene: RsbR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q92DC6
#5: Protein
RsbR protein


Mass: 31784.566 Da / Num. of mol.: 4 / Mutation: T175-TPO
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)
Strain: ATCC BAA-680 / CLIP 11262 / Gene: RsbR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q92DC6
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: stressosome complex RsbR and RsbS / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.5 MDa / Experimental value: NO
Source (natural)Organism: Listeria innocua Clip11262 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 8.5 / Details: pH 8.5
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
250 mMtrisC4H11NO31
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.19rc5_4047: phenix.real_space_refine / Classification: refinement
EM software
IDNameVersionCategory
12RELION33D reconstruction
13cryoSPARCV23D reconstruction
14PHENIX1.19rc5_4047model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32031 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more