[English] 日本語
Yorodumi- PDB-6ov2: Crystal structure of human claudin-9 in complex with Clostridium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ov2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human claudin-9 in complex with Clostridium perfringens entertoxin C-terminal domain in closed form | |||||||||
Components |
| |||||||||
Keywords | CELL ADHESION / Claudin / Enterotoxin / Tight junction protein / Transmembrane protein | |||||||||
Function / homology | Function and homology information calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / bicellular tight junction assembly / bicellular tight junction / cell junction / virus receptor activity / toxin activity / cell adhesion / intracellular membrane-bounded organelle / structural molecule activity ...calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / bicellular tight junction assembly / bicellular tight junction / cell junction / virus receptor activity / toxin activity / cell adhesion / intracellular membrane-bounded organelle / structural molecule activity / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Clostridium perfringens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||
Authors | Vecchio, A.J. / Stroud, R.M. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Claudin-9 structures reveal mechanism for toxin-induced gut barrier breakdown. Authors: Vecchio, A.J. / Stroud, R.M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ov2.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ov2.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ov2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ov2_validation.pdf.gz | 422.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ov2_full_validation.pdf.gz | 427.2 KB | Display | |
Data in XML | 6ov2_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 6ov2_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/6ov2 ftp://data.pdbj.org/pub/pdb/validation_reports/ov/6ov2 | HTTPS FTP |
-Related structure data
Related structure data | 6ov3C 3am2S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22862.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLDN9 / Cell line (production host): Tn5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O95484 |
---|---|
#2: Protein | Mass: 14795.565 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 194-319) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01558 |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 6.26 Å3/Da / Density % sol: 80.35 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 150 mM sodium acetate, sodium cacodylate, Bis-Tris propane, pH 4.5, 25% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 5, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11583 Å / Relative weight: 1 |
Reflection | Resolution: 3.16→70 Å / Num. obs: 30828 / % possible obs: 96.4 % / Redundancy: 9.6 % / Biso Wilson estimate: 137.73 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.0408 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3.16→3.24 Å / Redundancy: 6 % / Mean I/σ(I) obs: 0.18 / Num. unique obs: 2276 / CC1/2: 0.123 / Rrim(I) all: 6.589 / % possible all: 96.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model and PDB entry 3AM2 Resolution: 3.2→20.096 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.49
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 145.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→20.096 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|