[English] 日本語
Yorodumi
- EMDB-12676: Vibrio vulnificus stressosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12676
TitleVibrio vulnificus stressosome
Map data
Sample
  • Complex: stressosome complex of VvRsbR and VvRsbS
    • Protein or peptide: RsbS, negative regulator of sigma-B
    • Protein or peptide: Anti-anti-sigma factor
Keywordsstressosome / stress sensing / general stress response / Gram-negative / SIGNALING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsKaltwasser S / Heinz V
Funding supportEuropean Union, United Kingdom, 3 items
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 VM / Madej MG / Conway M / Lechner M / Riedel K / Bange G / Boyd A / Volker U / Lewis RJ / ...Authors: Heinz V / Jackel W / Kaltwasser S / Cutugno L / Bedrunka P / Graf A / Reder A / Michalik S / Dhople VM / Madej MG / Conway M / Lechner M / Riedel K / Bange G / Boyd A / Volker U / Lewis RJ / Marles-Wright J / Ziegler C / Pane-Farre J
History
DepositionMar 26, 2021-
Header (metadata) releaseApr 13, 2022-
Map releaseApr 13, 2022-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_12676.png

Downloads & links

-
Map

FileDownload / File: emd_12676.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.77 Å
Density
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.17149717 - 0.44632268
Average (Standard dev.)0.0010252036 (±0.020204483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 442.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : stressosome complex of VvRsbR and VvRsbS

EntireName: stressosome complex of VvRsbR and VvRsbS
Components
  • Complex: stressosome complex of VvRsbR and VvRsbS
    • Protein or peptide: RsbS, negative regulator of sigma-B
    • Protein or peptide: Anti-anti-sigma factor

-
Supramolecule #1: stressosome complex of VvRsbR and VvRsbS

SupramoleculeName: stressosome complex of VvRsbR and VvRsbS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio vulnificus (bacteria)

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

MacromoleculeName: RsbS, negative regulator of sigma-B / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Vibrio vulnificus (bacteria)
Molecular weightTheoretical: 12.390511 KDa
Recombinant expressionOrganism: Vibrio vulnificus (bacteria)
SequenceString:
MQSAISISKL QDVLIASVQV DLTESTLRDF SLDLLDAVKS TRAKGVMIEL SGVKTLDGES MHSLLDVVKT VEVMGRRCLL VGLRPGVVI GLMDIGIDLA STLCVADLEQ GFLYLE

UniProtKB: RsbS, negative regulator of sigma-B

-
Macromolecule #2: Anti-anti-sigma factor

MacromoleculeName: Anti-anti-sigma factor / type: protein_or_peptide / ID: 2 / Number of copies: 48 / Enantiomer: LEVO
Source (natural)Organism: Vibrio vulnificus (bacteria)
Molecular weightTheoretical: 34.606043 KDa
Recombinant expressionOrganism: Vibrio vulnificus (bacteria)
SequenceString: MSLGSVLNKV EDADELLKLH DLTEADLALI RKFGQIMVPK LDEYVKHFYD WLRNTPEYEQ YFGDAQKLQR VQDSQVRYWK TFFDARIDS AYLKERRDVG EIHARVGLPL PTYFAGMNIS MVIFTKRMYD GSLYSDEYSS LVTAFTKLLH LDTTIVVDTY S RLINKRIS ...String:
MSLGSVLNKV EDADELLKLH DLTEADLALI RKFGQIMVPK LDEYVKHFYD WLRNTPEYEQ YFGDAQKLQR VQDSQVRYWK TFFDARIDS AYLKERRDVG EIHARVGLPL PTYFAGMNIS MVIFTKRMYD GSLYSDEYSS LVTAFTKLLH LDTTIVVDTY S RLINKRIS EQSEALLAMS TPVTMIWQDI LMLPIVGIID SKRAQDIMSA VLNKISENRA KIFIMDISGV AVVDTAVANH FI KITKATK LMGCDCLVSG VSPSIARTMV QLGINVGEVR TNATLRDALE NAFKIVGLTV SGLKHFPHE

UniProtKB: Anti-anti-sigma factor

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris/HCl
150.0 mMsodium chlorideNaCl
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.5 sec. / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 59000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 230784 / Details: template-based auto picking
Startup modelType of model: OTHER / Details: generated from the dataset
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 35647
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: RELION

+
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