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Yorodumi- PDB-3x29: CRYSTAL STRUCTURE of MOUSE CLAUDIN-19 IN COMPLEX with C-TERMINAL ... -
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-Basic information
Entry | Database: PDB / ID: 3x29 | ||||||
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Title | CRYSTAL STRUCTURE of MOUSE CLAUDIN-19 IN COMPLEX with C-TERMINAL FRAGMENT OF CLOSTRIDIUM PERFRINGENS ENTEROTOXIN | ||||||
Components |
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Keywords | CELL ADHESION / TOXIN-CELL ADHESION COMPLEX / TIGHT JUNCTION / ENTEROTOXIN / MEMBRANE PROTEIN / RECEPTOR BINDING | ||||||
Function / homology | Function and homology information positive regulation of cell junction assembly / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / tight junction organization / : / regulation of transepithelial transport / negative regulation of wound healing / bicellular tight junction assembly / apical junction assembly / neuronal action potential propagation / apical junction complex ...positive regulation of cell junction assembly / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / tight junction organization / : / regulation of transepithelial transport / negative regulation of wound healing / bicellular tight junction assembly / apical junction assembly / neuronal action potential propagation / apical junction complex / bicellular tight junction / negative regulation of cell migration / cell junction / toxin activity / basolateral plasma membrane / membrane => GO:0016020 / cell adhesion / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / perinuclear region of cytoplasm / structural molecule activity / extracellular region / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||
Authors | Saitoh, Y. / Suzuki, H. / Tani, K. / Nishikawa, K. / Irie, K. / Ogura, Y. / Tamura, A. / Tsukita, S. / Fujiyoshi, Y. | ||||||
Citation | Journal: Science / Year: 2015 Title: Structural insight into tight junction disassembly by Clostridium perfringens enterotoxin Authors: Saitoh, Y. / Suzuki, H. / Tani, K. / Nishikawa, K. / Irie, K. / Ogura, Y. / Tamura, A. / Tsukita, S. / Fujiyoshi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x29.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x29.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 3x29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/3x29 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/3x29 | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19217.262 Da / Num. of mol.: 2 / Fragment: TM REGION, UNP residues 1-185 / Mutation: C104A, C183A, C184A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cldn19 / Plasmid: PFASTBAC1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q9ET38 #2: Protein | Mass: 13329.830 Da / Num. of mol.: 2 / Fragment: UNP residues 203-319 / Mutation: S313A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01558 |
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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: 4.98 Å3/Da / Density % sol: 75.28 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 17.5% PEG1500, 100mM sodium citrate, 100mM Mg(NO3)2, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 11, 2014 |
Radiation | Monochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→34.738 Å / Num. obs: 14027 / % possible obs: 97.27 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 3.7→3.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.1 / % possible all: 92.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CLDN15 AND CPE WITH 202 N-TERM RESIDUES DELETED Resolution: 3.7→34.738 Å / SU ML: 0.57 / σ(F): 1.5 / Phase error: 29.45 / 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: 3.7→34.738 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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