[English] 日本語
Yorodumi- PDB-1obz: Crystal structure of the complex of the PDZ tandem of syntenin wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1obz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the complex of the PDZ tandem 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 / syndecan binding / neurexin family protein binding / Neurofascin interactions / presynapse assembly / cytoskeletal anchor activity ...interleukin-5 receptor activity / regulation of interleukin-5 production / interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / Neurofascin interactions / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / interleukin-5-mediated signaling pathway / positive regulation of exosomal secretion / positive regulation of leukocyte proliferation / frizzled binding / negative regulation of receptor internalization / inflammatory response to antigenic stimulus / protein targeting to membrane / cytokine receptor activity / Ephrin signaling / RIPK1-mediated regulated necrosis / positive regulation of transforming growth factor beta receptor signaling pathway / growth factor binding / regulation of mitotic cell cycle / cytokine binding / positive regulation of phosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / positive regulation of epithelial to mesenchymal transition / cell adhesion molecule binding / protein sequestering activity / phosphatidylinositol-4,5-bisphosphate binding / ionotropic glutamate receptor binding / ephrin receptor binding / adherens junction / positive regulation of JNK cascade / Regulation of necroptotic cell death / cytokine-mediated signaling pathway / azurophil granule lumen / extracellular vesicle / melanosome / presynapse / RAF/MAP kinase cascade / positive regulation of cell growth / nuclear membrane / actin cytoskeleton organization / Ras protein signal transduction / chemical synaptic transmission / receptor complex / blood microparticle / cytoskeleton / 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 / endoplasmic reticulum membrane / Neutrophil degranulation / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1obz.cif.gz | 147.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1obz.ent.gz | 115.7 KB | Display | PDB format |
PDBx/mmJSON format | 1obz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1obz_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1obz_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 1obz_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 1obz_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/1obz ftp://data.pdbj.org/pub/pdb/validation_reports/ob/1obz | HTTPS FTP |
-Related structure data
Related structure data | 1nteC 1obxC 1obyC 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 |
| |||||||||
Details | THE TRIMER IS FORMED BY THE COMPLEX OF CHAINS A AND BWITH ONE MOLECULE OF CHAIN P |
-Components
#1: Protein | Mass: 18018.688 Da / Num. of mol.: 2 / Fragment: PDZ2, RESIDUES 113-273 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 | ChemComp-ACT / #4: 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: 2.2 Å3/Da / Density % sol: 43.7 % |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 4.6 Details: SITTING DROP WITH 0.2 M SODIUM ACETATE, PH 4.6 28% PEG4000, 0.2 M AMMONIUM ACETATE |
-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: Jan 20, 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: 1.7→50 Å / Num. obs: 112090 / % possible obs: 95.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.13 / % possible all: 72.4 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 50 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.13 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N99 Resolution: 1.7→64.55 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.207 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.117 / 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 PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.64 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→64.55 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|