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Yorodumi- PDB-6h6g: Crystal Structure of TcdB2-TccC3 without hypervariable C-terminal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h6g | ||||||
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Title | Crystal Structure of TcdB2-TccC3 without hypervariable C-terminal region | ||||||
Components | TcdB2,TccC3 | ||||||
Keywords | TOXIN / Tc toxin / ABC toxin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Photorhabdus luminescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å | ||||||
Authors | Gatsogiannis, C. / Merino, F. / Roderer, D. / Balchin, D. / Schubert, E. / Kuhlee, A. / Hayer-Hartl, M. / Raunser, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nature / Year: 2018 Title: Tc toxin activation requires unfolding and refolding of a β-propeller. Authors: Christos Gatsogiannis / Felipe Merino / Daniel Roderer / David Balchin / Evelyn Schubert / Anne Kuhlee / Manajit Hayer-Hartl / Stefan Raunser / Abstract: Tc toxins secrete toxic enzymes into host cells using a unique syringe-like injection mechanism. They are composed of three subunits, TcA, TcB and TcC. TcA forms the translocation channel and the TcB- ...Tc toxins secrete toxic enzymes into host cells using a unique syringe-like injection mechanism. They are composed of three subunits, TcA, TcB and TcC. TcA forms the translocation channel and the TcB-TcC heterodimer functions as a cocoon that shields the toxic enzyme. Binding of the cocoon to the channel triggers opening of the cocoon and translocation of the toxic enzyme into the channel. Here we show in atomic detail how the assembly of the three components activates the toxin. We find that part of the cocoon completely unfolds and refolds into an alternative conformation upon binding. The presence of the toxic enzyme inside the cocoon is essential for its subnanomolar binding affinity for the TcA subunit. The enzyme passes through a narrow negatively charged constriction site inside the cocoon, probably acting as an extruder that releases the unfolded protein with its C terminus first into the translocation channel. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h6g.cif.gz | 787.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h6g.ent.gz | 653.9 KB | Display | PDB format |
PDBx/mmJSON format | 6h6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h6g_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 6h6g_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 6h6g_validation.xml.gz | 69.3 KB | Display | |
Data in CIF | 6h6g_validation.cif.gz | 93.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/6h6g ftp://data.pdbj.org/pub/pdb/validation_reports/h6/6h6g | HTTPS FTP |
-Related structure data
Related structure data | 0149C 0150C 6h6eC 6h6fC 4o9xS 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: 243770.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: tcdB2, TccC3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8GF99, UniProt: Q8GF97 |
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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: 4.5 Å3/Da / Density % sol: 72.66 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M tri-sodium citrate pH 5.5, 10 % PEG 8000, 10 % ethylenglycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97794 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97794 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 87208 / % possible obs: 99.9 % / Redundancy: 20 % / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 3→3.08 Å / Rmerge(I) obs: 0.5751 / Rpim(I) all: 0.129 / Rrim(I) all: 0.5895 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O9X Resolution: 3.004→48.639 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.004→48.639 Å
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Refine LS restraints |
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LS refinement shell |
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