+Open data
-Basic information
Entry | Database: PDB / ID: 7o0i | ||||||||||||
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Title | Vibrio vulnificus stressosome | ||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / stressosome / stress sensing / general stress response / Gram-negative | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.3 Å | ||||||||||||
Authors | Kaltwasser, S. / Heinz, V. / Madej, M.G. / Pane-Farre, J. / Ziegler, C. | ||||||||||||
Funding support | European Union, United Kingdom, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o0i.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7o0i.ent.gz | 726.3 KB | Display | PDB format |
PDBx/mmJSON format | 7o0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o0i_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7o0i_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7o0i_validation.xml.gz | 114.6 KB | Display | |
Data in CIF | 7o0i_validation.cif.gz | 200 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/7o0i ftp://data.pdbj.org/pub/pdb/validation_reports/o0/7o0i | HTTPS FTP |
-Related structure data
Related structure data | 12676MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | 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 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: stressosome complex of VvRsbR and VvRsbS / Type: COMPLEX / Entity ID: all / Source: NATURAL | |||||||||||||||
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Source (natural) | Organism: Vibrio vulnificus (bacteria) | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid type: Quantifoil | |||||||||||||||
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 5500 nm / Nominal defocus min: 1700 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 72 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Movie frames/image: 24 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 230784 / Details: template-based auto picking | ||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35647 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 268.97 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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