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- EMDB-12676: Vibrio vulnificus stressosome -

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Open data


ID or keywords:

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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 / 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

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Structure visualization

Supplemental images

emd_12676.png

Downloads & links

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Map

FileDownload / File: emd_12676.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 250 pix.
= 442.5 Å		1.77 Å/pix.
x 250 pix.
= 442.5 Å		1.77 Å/pix.
x 250 pix.
= 442.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

Histogram

Histogram (log scale)
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 °

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Supplemental data

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Sample components

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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

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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)

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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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

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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

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