[English] 日本語
Yorodumi- PDB-1obx: Crystal structure of the complex of PDZ2 of syntenin with an inte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1obx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the complex of PDZ2 of syntenin with an interleukin 5 receptor alpha peptide. | ||||||
Components |
| ||||||
Keywords | CELL ADHESION / ADHESION-COMPLEX / PDZ DOMAIN / SIGNAL TRANSDUCTION / NUCLEAR PROTEIN | ||||||
Function / homology | Function and homology information interleukin-5 receptor activity / regulation of interleukin-5 production / interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / neurexin family protein binding / syndecan binding / Neurofascin interactions / presynapse assembly / substrate-dependent cell migration, cell extension ...interleukin-5 receptor activity / regulation of interleukin-5 production / interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / neurexin family protein binding / syndecan binding / Neurofascin interactions / presynapse assembly / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity / interleukin-5-mediated signaling pathway / positive regulation of exosomal secretion / positive regulation of leukocyte proliferation / negative regulation of receptor internalization / frizzled binding / inflammatory response to antigenic stimulus / protein targeting to membrane / cytokine receptor activity / Ephrin signaling / RIPK1-mediated regulated necrosis / cytokine binding / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of mitotic cell cycle / growth factor binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / positive regulation of epithelial to mesenchymal transition / Interleukin receptor SHC signaling / positive regulation of phosphorylation / ionotropic glutamate receptor binding / phosphatidylinositol-4,5-bisphosphate binding / cell adhesion molecule binding / ephrin receptor binding / protein sequestering activity / adherens junction / positive regulation of JNK cascade / Regulation of necroptotic cell death / cytokine-mediated signaling pathway / extracellular vesicle / azurophil granule lumen / melanosome / presynapse / chemical synaptic transmission / actin cytoskeleton organization / RAF/MAP kinase cascade / positive regulation of cell growth / blood microparticle / nuclear membrane / Ras protein signal transduction / cytoskeleton / receptor complex / positive regulation of cell migration / intracellular signal transduction / membrane raft / protein heterodimerization activity / external side of plasma membrane / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Kang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Molecular Roots of Degenerate Specificity in Syntenin'S Pdz2 Domain: Reassessment of the Pdz Recognition Paradigm Authors: Kang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1obx.cif.gz | 51.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1obx.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 1obx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/1obx ftp://data.pdbj.org/pub/pdb/validation_reports/ob/1obx | HTTPS FTP |
---|
-Related structure data
Related structure data | 1nteC 1obyC 1obzC 1n99S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 8394.598 Da / Num. of mol.: 1 / Fragment: PDZ2, RESIDUES 197-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O00560 | ||||||
---|---|---|---|---|---|---|---|
#2: Protein/peptide | Mass: 938.975 Da / Num. of mol.: 1 / Fragment: LAST 8 RESIDUES, RESIDUES 413-420 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q01344 | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | MOL_ID 1: FUNCTIONS AS AN ADAPTER PROTEIN. MAY ALSO FUNCTION TO COUPLE SYNDECANS TO CYTOSKELETAL ...MOL_ID 1: FUNCTIONS AS AN ADAPTER PROTEIN. MAY ALSO FUNCTION TO COUPLE SYNDECANS TO CYTOSKELET | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 38.1 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 Details: SITTING DROP 0.1 M HEPES, PH 7.0, 1.6 M AMMONIUM SULFATE, 20 MM COCL2, 0.2 M MGSO4 WITH MICROSEEDIN | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 K / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 29, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→20 Å / Num. obs: 155256 / % possible obs: 95.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.0051 / Net I/σ(I): 33.5 |
Reflection shell | Resolution: 1.25→1.29 Å / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.15 / % possible all: 75 |
Reflection | *PLUS Highest resolution: 1.25 Å / Lowest resolution: 20 Å / Num. measured all: 20850 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 75 % / Num. unique obs: 1611 / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.15 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N99 Resolution: 1.35→19.39 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.922 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.05 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→19.39 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|