+Open data
-Basic information
Entry | Database: PDB / ID: 6ek8 | ||||||
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Title | YaxB from Yersinia enterocolitica | ||||||
Components | YaxB | ||||||
Keywords | MEMBRANE PROTEIN / pathogens / pore forming toxins / alpha-helical / adventitious membrane protein | ||||||
Function / homology | : / Alpha-xenorhabdolysin family binary toxin subunit B Function and homology information | ||||||
Biological species | Yersinia enterocolitica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | ||||||
Authors | Braeuning, B. / Groll, M. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. Authors: Bastian Bräuning / Eva Bertosin / Florian Praetorius / Christian Ihling / Alexandra Schatt / Agnes Adler / Klaus Richter / Andrea Sinz / Hendrik Dietz / Michael Groll / Abstract: Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, ...Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures. YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the molecular basis for its two-component lytic mechanism remains elusive. Here, we present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy map of the YaxAB complex. Our structures reveal a pore predominantly composed of decamers of YaxA-YaxB heterodimers. Both subunits bear membrane-active moieties, but only YaxA is capable of binding to membranes by itself. YaxB can subsequently be recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices. Pore formation can progress by further oligomerization of YaxA-YaxB dimers. Our results allow for a comparison between pore assemblies belonging to the wider ClyA-like family of α-PFTs, highlighting diverse pore architectures. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ek8.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ek8.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ek8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ek8_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 6ek8_full_validation.pdf.gz | 431.7 KB | Display | |
Data in XML | 6ek8_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 6ek8_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/6ek8 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/6ek8 | HTTPS FTP |
-Related structure data
Related structure data | 3885C 6ek4SC 6ek7C 6el1C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39248.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: YE1985 / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / References: UniProt: A1JM52 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.37 Å3/Da / Density % sol: 77.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.2 M Na/K-phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. obs: 5633 / % possible obs: 98.7 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13 |
Reflection shell | Resolution: 4→4.1 Å / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.73 / % possible all: 99.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EK4 Resolution: 4→48.82 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.928 / SU B: 155.607 / SU ML: 0.904 / Cross valid method: THROUGHOUT / ESU R Free: 0.847 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 196.051 Å2
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Refinement step | Cycle: 1 / Resolution: 4→48.82 Å
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Refine LS restraints |
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