[English] 日本語
Yorodumi
- EMDB-4508: Cryo em structure of the Listeria stressosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4508
TitleCryo em structure of the Listeria stressosome
Map data
Sample
  • Complex: Listeria Stressosome Core
    • Organelle or cellular component: RsbR
      • Protein or peptide: RsbR protein
      • Protein or peptide: RsbR protein
      • Protein or peptide: RsbR protein,RsbR protein
      • Protein or peptide: RsbR protein
    • Organelle or cellular component: RsbS
      • Protein or peptide: RsbS protein
KeywordsStressosome complex / stress response machine / Bacteria stress sensor / ANTIMICROBIAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.21 Å
AuthorsWilliams AH / Redzej A
Funding support United Kingdom, France, 2 items
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, 2018-
Header (metadata) releaseJul 31, 2019-
Map releaseAug 21, 2019-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.011
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.011
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6qcm
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6qcm
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4508.png

Downloads & links

-
Map

FileDownload / File: emd_4508.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.1.061.061.06
CCP4 map header410410410
EM Navigator Movie #11.061.061.06
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011 / Movie #1: 0.011
Minimum - Maximum-0.06522523 - 0.11754276
Average (Standard dev.)0.00035815538 (±0.003878759)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions410410410
Spacing410410410
CellA=B=C: 434.59998 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-0.0650.1180.000

-
Supplemental data

-
Sample components

-
Entire : Listeria Stressosome Core

EntireName: Listeria Stressosome Core
Components
  • Complex: Listeria Stressosome Core
    • Organelle or cellular component: RsbR
      • Protein or peptide: RsbR protein
      • Protein or peptide: RsbR protein
      • Protein or peptide: RsbR protein,RsbR protein
      • Protein or peptide: RsbR protein
    • Organelle or cellular component: RsbS
      • Protein or peptide: RsbS protein

-
Supramolecule #1: Listeria Stressosome Core

SupramoleculeName: Listeria Stressosome Core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: The subcomponents are, RsbR and RsbS
Molecular weightTheoretical: 1.8 MDa

-
Supramolecule #2: RsbR

SupramoleculeName: RsbR / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #4-#5
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)

-
Supramolecule #3: RsbS

SupramoleculeName: RsbS / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)

-
Macromolecule #1: RsbR protein

MacromoleculeName: RsbR protein / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)
Molecular weightTheoretical: 13.9445 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
SALQELSAPL LPIFEKISVM PLIGTIDTER AKLIIENLLI GVVKNRSEVV LIDITGVPVV DTMVAHHIIQ ASEAVRLVGC QAMLVGIRP EIAQTIVNLG IELDQIITTN TMKKGMERAL ALTNREIVE

UniProtKB: RsbR protein

-
Macromolecule #2: RsbR protein

MacromoleculeName: RsbR protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)
Molecular weightTheoretical: 14.073681 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
KSALQELSAP LLPIFEKISV MPLIGTIDTE RAKLIIENLL IGVVKNRSEV VLIDITGVPV VDTMVAHHII QASEAVRLVG CQAMLVGIR PEIAQTIVNL GIELDQIITT NTMKKGMERA LALTNREIVE

UniProtKB: RsbR protein

-
Macromolecule #3: RsbS protein

MacromoleculeName: RsbS protein / type: protein_or_peptide / ID: 3 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)
Molecular weightTheoretical: 12.606707 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MGIPILKLGE CLLISIQSEL DDHTAVEFQE DLLAKIHETS ARGVVIDITS IDFIDSFIAK ILGDVVSMSK LMGAKVVVTG IQPAVAITL IELGITFSGV LSAMDLESGL EKLKQELGE

UniProtKB: RsbS protein

-
Macromolecule #4: RsbR protein,RsbR protein

MacromoleculeName: RsbR protein,RsbR protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)
Molecular weightTheoretical: 13.479988 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
EKTVSIQKSA LQELSAPLLP IFEKISVMPL IGTIDTERAK LIIENLLIGV VKNRSEVVLI DITGVPVVDT MVAHHIIQAS EAVRLVGCQ AMLVGIRPEQ IITTNTMKKG MERALALTNR EIVE

UniProtKB: RsbR protein, RsbR protein

-
Macromolecule #5: RsbR protein

MacromoleculeName: RsbR protein / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)
Molecular weightTheoretical: 14.860573 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
EKTVSIQKSA LQELSAPLLP IFEKISVMPL IGTIDTERAK LIIENLLIGV VKNRSEVVLI DITGVPVVDT MVAHHIIQAS EAVRLVGCQ AMLVGIRPEI AQTIVNLGIE LDQIITTNTM KKGMERALAL TNREIVE

UniProtKB: RsbR protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.02 mg/mL
BufferpH: 8.5
GridModel: Quantifoil R2/2 / Material: COPPER/PALLADIUM / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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

+
Image processing

Particle selectionNumber selected: 200000
Startup modelType of model: OTHER
Details: Initial model was calculated ab initio in cryoSPARC using particles selected after 3 rounds of 2D classification.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 78000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

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

+
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://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