+Open data
-Basic information
Entry | Database: PDB / ID: 1pfo | ||||||
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Title | PERFRINGOLYSIN O | ||||||
Components | PERFRINGOLYSIN O | ||||||
Keywords | TOXIN / THIOL-ACTIVATED CYTOLYSIN / HEMOLYSIS / CYTOLYSIS | ||||||
Function / homology | Function and homology information hemolysis in another organism / cholesterol binding / toxin activity / membrane => GO:0016020 / host cell plasma membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å | ||||||
Authors | Rossjohn, J. / Parker, M.W. | ||||||
Citation | Journal: Cell / Year: 1997 Title: Structure of a cholesterol-binding, thiol-activated cytolysin and a model of its membrane form. Authors: J Rossjohn / S C Feil / W J McKinstry / R K Tweten / M W Parker / Abstract: The mechanisms by which proteins gain entry into membranes is a fundamental problem in biology. Here, we present the first crystal structure of a thiol-activated cytolysin, perfringolysin O, a member ...The mechanisms by which proteins gain entry into membranes is a fundamental problem in biology. Here, we present the first crystal structure of a thiol-activated cytolysin, perfringolysin O, a member of a large family of toxins that kill eukaryotic cells by punching holes in their membranes. The molecule adopts an unusually elongated shape rich in beta sheet. We have used electron microscopy data to construct a detailed model of the membrane channel form of the toxin. The structures reveal a novel mechanism for membrane insertion. Surprisingly, the toxin receptor, cholesterol, appears to play multiple roles: targeting, promotion of oligomerization, triggering a membrane insertion competent form, and stabilizing the membrane pore. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pfo.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pfo.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 1pfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/1pfo ftp://data.pdbj.org/pub/pdb/validation_reports/pf/1pfo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55831.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) Description: SECRETED AS A MONOMER, FORMS MEMBRANE-BOUND OLIGOMERS Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P19995, UniProt: P0C2E9*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 66 % | |||||||||||||||||||||||||
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Crystal grow | pH: 8.4 / Details: 10% PEG 20000, 100MM BICINE, PH 8.4, 2% DIOXANE | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 8.7 / Method: vapor diffusion, hanging drop / Details: Feil, S.C., (1996) FEBS Lett., 397, 290. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Detector: FILM / Date: Apr 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 37231 / % possible obs: 86 % / Redundancy: 3.26 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.1→2.17 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.1 / % possible all: 87.1 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE FIRST NINE RESIDUES HAVE HIGH MOBILITY, AND THE CORRESPONDING DENSITY WAS SMEARED OUT. THE R FREE WAS LOWER WHEN THESE RESIDUES WERE INCLUDED IN THE MODEL. UNCERTAINTY IN PLACEMENT AROUND RESIDUE 60.
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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