[English] 日本語
Yorodumi- PDB-5i7z: Crystal structure of a Par-6 PDZ-Crumbs 3 C-terminal peptide complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i7z | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a Par-6 PDZ-Crumbs 3 C-terminal peptide complex | |||||||||
Components |
| |||||||||
Keywords | SIGNALING PROTEIN / PDZ / cell polarity | |||||||||
Function / homology | Function and homology information positive regulation of cell junction assembly / CDC42 GTPase cycle / RAC1 GTPase cycle / RHOV GTPase cycle / terminal branching, open tracheal system / subapical complex / establishment or maintenance of neuroblast polarity / branching involved in open tracheal system development / zonula adherens assembly / establishment of neuroblast polarity ...positive regulation of cell junction assembly / CDC42 GTPase cycle / RAC1 GTPase cycle / RHOV GTPase cycle / terminal branching, open tracheal system / subapical complex / establishment or maintenance of neuroblast polarity / branching involved in open tracheal system development / zonula adherens assembly / establishment of neuroblast polarity / RHOU GTPase cycle / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Asymmetric localization of PCP proteins / establishment or maintenance of polarity of embryonic epithelium / muscle cell postsynaptic specialization / border follicle cell migration / Tight junction interactions / asymmetric neuroblast division / morphogenesis of a polarized epithelium / apical cortex / bicellular tight junction assembly / apical protein localization / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of smoothened signaling pathway / centrosome cycle / positive regulation of filopodium assembly / protein kinase inhibitor activity / bicellular tight junction / positive regulation of lamellipodium assembly / synapse assembly / protein localization to plasma membrane / terminal bouton / SH3 domain binding / cell junction / cell cortex / membrane => GO:0016020 / apical plasma membrane / protein domain specific binding / protein-containing complex / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.801 Å | |||||||||
Authors | Whitney, D.S. / Peterson, F.C. / Prehoda, K.E. / Volkman, B.F. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Binding of Crumbs to the Par-6 CRIB-PDZ Module Is Regulated by Cdc42. Authors: Whitney, D.S. / Peterson, F.C. / Kittell, A.W. / Egner, J.M. / Prehoda, K.E. / Volkman, B.F. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5i7z.cif.gz | 35.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5i7z.ent.gz | 22.9 KB | Display | PDB format |
PDBx/mmJSON format | 5i7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/5i7z ftp://data.pdbj.org/pub/pdb/validation_reports/i7/5i7z | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 10266.793 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 158-253) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: par-6, CG5884, Dmel_CG5884 / Plasmid: PBH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O97111 |
---|---|
#2: Protein/peptide | Mass: 967.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BUF7*PLUS |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.43 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 26% PEG 6000, 100 mM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 10639 / % possible obs: 95.6 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 43.4 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 1.9 / % possible all: 70.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.801→38.448 Å / FOM work R set: 0.7847 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.85 Å2 / Biso mean: 37.11 Å2 / Biso min: 16.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.801→38.448 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
|