[English] 日本語
Yorodumi- PDB-6akf: Crystal structure of mouse claudin-3 P134A mutant in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6akf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of mouse claudin-3 P134A mutant in complex with C-terminal fragment of Clostridium perfringens enterotoxin | ||||||
Components |
| ||||||
Keywords | MEMBRANE PROTEIN/TOXIN / Cell adhesion / Tight junction / MEMBRANE PROTEIN-TOXIN complex | ||||||
Function / homology | Function and homology information cell junction maintenance / establishment of endothelial blood-brain barrier / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / response to Gram-positive bacterium / regulation of transepithelial transport / regulation of membrane permeability / negative regulation of wound healing / positive regulation of bicellular tight junction assembly / epithelial cell morphogenesis / bicellular tight junction assembly ...cell junction maintenance / establishment of endothelial blood-brain barrier / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / response to Gram-positive bacterium / regulation of transepithelial transport / regulation of membrane permeability / negative regulation of wound healing / positive regulation of bicellular tight junction assembly / epithelial cell morphogenesis / bicellular tight junction assembly / apicolateral plasma membrane / tight junction / regulation of cell morphogenesis / positive regulation of wound healing / lateral plasma membrane / bicellular tight junction / negative regulation of cell migration / cell-cell junction / toxin activity / actin cytoskeleton organization / response to ethanol / cell adhesion / response to hypoxia / positive regulation of cell migration / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / structural molecule activity / protein-containing complex / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å | ||||||
Authors | Nakamura, S. / Irie, K. / Fujiyoshi, Y. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Morphologic determinant of tight junctions revealed by claudin-3 structures. Authors: Nakamura, S. / Irie, K. / Tanaka, H. / Nishikawa, K. / Suzuki, H. / Saitoh, Y. / Tamura, A. / Tsukita, S. / Fujiyoshi, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6akf.cif.gz | 231.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6akf.ent.gz | 185.1 KB | Display | PDB format |
PDBx/mmJSON format | 6akf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6akf_validation.pdf.gz | 494.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6akf_full_validation.pdf.gz | 512.6 KB | Display | |
Data in XML | 6akf_validation.xml.gz | 41.2 KB | Display | |
Data in CIF | 6akf_validation.cif.gz | 56.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/6akf ftp://data.pdbj.org/pub/pdb/validation_reports/ak/6akf | HTTPS FTP |
-Related structure data
Related structure data | 6akeSC 6akgC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
4 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19880.467 Da / Num. of mol.: 4 / Fragment: UNP residues 1-183 / Mutation: P134A,C103A, C106A, C181A, C182A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cldn3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Z0G9 #2: Protein | Mass: 13329.830 Da / Num. of mol.: 4 / 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) / References: UniProt: P01558 Sequence details | AUTHORS STATE THAT THE N-TERMINAL RESIDUES GHMASGS IN A AND C CHAINS ARE DERIVED FROM THE TEV ...AUTHORS STATE THAT THE N-TERMINAL RESIDUES GHMASGS IN A AND C CHAINS ARE DERIVED FROM THE TEV PROTEASE CLEAVAGE SITE AND LINKER AND THAT GLY201 AND SER202 IN B AND D CHAINS ARE DERIVED FROM THE THROMBIN CLEAVAGE SITE. | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.57 Å3/Da / Density % sol: 77.94 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 7 / Details: HEPES, Sodium acetate, Magnesium nitrate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→46.66 Å / Num. obs: 25301 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 95.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09076 / Rpim(I) all: 0.05924 / Rrim(I) all: 0.1089 / Net I/σ(I): 8.17 |
Reflection shell | Resolution: 3.9→4.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.032 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 2529 / CC1/2: 0.575 / Rpim(I) all: 0.682 / Rrim(I) all: 1.244 / % possible all: 99.49 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AKE Resolution: 3.9→46.66 Å / SU ML: 0.6606 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.9559
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 119.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.9→46.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|