[English] 日本語
Yorodumi
- PDB-7o0i: Vibrio vulnificus stressosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o0i
TitleVibrio vulnificus stressosome
Components
  • Anti-anti-sigma factor
  • RsbS, negative regulator of sigma-B
KeywordsSIGNALING PROTEIN / stressosome / stress sensing / general stress response / Gram-negative
Function / homology
Function and homology information


oxygen binding / oxidoreductase activity / heme binding
Similarity search - Function
Globin-sensor domain / Protoglobin / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / Globin/Protoglobin / Globin-like superfamily
Similarity search - Domain/homology
Anti-anti-sigma factor / RsbS, negative regulator of sigma-B
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsKaltwasser, S. / Heinz, V. / Madej, M.G. / Pane-Farre, J. / Ziegler, C.
Funding supportEuropean Union, United Kingdom, 3items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission721456European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/G001553/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L024209/1 United Kingdom
CitationJournal: Commun Biol / Year: 2022
Title: The Vibrio vulnificus stressosome is an oxygen-sensor involved in regulating iron metabolism
Authors: Heinz, V. / Jackel, W. / Kaltwasser, S. / Cutugno, L. / Bedrunka, P. / Graf, A. / Reder, A. / Michalik, S. / Dhople, V.M. / Madej, M.G. / Conway, M. / Lechner, M. / Riedel, K. / Bange, G. / ...Authors: Heinz, V. / Jackel, W. / Kaltwasser, S. / Cutugno, L. / Bedrunka, P. / Graf, A. / Reder, A. / Michalik, S. / Dhople, V.M. / Madej, M.G. / Conway, M. / Lechner, M. / Riedel, K. / Bange, G. / Boyd, A. / Volker, U. / Lewis, R.J. / Marles-Wright, J. / Ziegler, C. / Pane-Farre, J.
History
DepositionMar 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / em_imaging / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _pdbx_audit_support.country

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,809,77660
Polymers1,809,77660
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
RsbS, negative regulator of sigma-B


Mass: 12390.511 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: CRN52_18815 / Production host: Vibrio vulnificus (bacteria) / References: UniProt: A0A2S3QZH9
#2: Protein ...
Anti-anti-sigma factor


Mass: 34606.043 Da / Num. of mol.: 48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: CRN52_18810, CRN58_24315 / Production host: Vibrio vulnificus (bacteria) / References: UniProt: A0A1W6M9Q5

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: stressosome complex of VvRsbR and VvRsbS / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Vibrio vulnificus (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris/HCl1
2150 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 5500 nm / Nominal defocus min: 1700 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 72 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 24

-
Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1RELIONparticle selection
11CTFFIND3CTF correction
16RELIONclassification
18RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 230784 / Details: template-based auto picking
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35647 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 268.97 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01536324
ELECTRON MICROSCOPYf_angle_d2.57350520
ELECTRON MICROSCOPYf_dihedral_angle_d4.6957296
ELECTRON MICROSCOPYf_chiral_restr0.1696960
ELECTRON MICROSCOPYf_plane_restr0.0147296

+
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