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Yorodumi- PDB-1ybo: Crystal structure of the PDZ tandem of human syntenin with syndec... -
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-Basic information
Entry | Database: PDB / ID: 1ybo | ||||||
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Title | Crystal structure of the PDZ tandem of human syntenin with syndecan peptide | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / PDZ domain / scaffolding protein / adhesion complex | ||||||
Function / homology | Function and homology information Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / regulation of fibroblast migration / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / interleukin-5 receptor complex / interleukin-5 receptor binding ...Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / regulation of fibroblast migration / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / inner ear receptor cell stereocilium organization / HS-GAG degradation / syndecan binding / neurexin family protein binding / Neurofascin interactions / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / costamere / frizzled binding / negative regulation of receptor internalization / protein targeting to membrane / Ephrin signaling / ureteric bud development / RIPK1-mediated regulated necrosis / Syndecan interactions / thrombospondin receptor activity / RSV-host interactions / positive regulation of transforming growth factor beta receptor signaling pathway / growth factor binding / positive regulation of focal adhesion assembly / Respiratory syncytial virus (RSV) attachment and entry / fibronectin binding / negative regulation of T cell proliferation / positive regulation of epithelial to mesenchymal transition / Retinoid metabolism and transport / positive regulation of phosphorylation / positive regulation of stress fiber assembly / cell adhesion molecule binding / regulation of mitotic cell cycle / phosphatidylinositol-4,5-bisphosphate binding / protein sequestering activity / ephrin receptor binding / ionotropic glutamate receptor binding / lysosomal lumen / neural tube closure / Cell surface interactions at the vascular wall / adherens junction / protein kinase C binding / positive regulation of JNK cascade / wound healing / Regulation of necroptotic cell death / Golgi lumen / azurophil granule lumen / melanosome / extracellular vesicle / cell migration / presynapse / actin cytoskeleton organization / positive regulation of cell growth / chemical synaptic transmission / nuclear membrane / blood microparticle / Ras protein signal transduction / Attachment and Entry / cytoskeleton / intracellular signal transduction / positive regulation of cell migration / protein heterodimerization activity / membrane raft / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Grembecka, J. / Cooper, D.R. / Cierpicki, T. / Kang, B.S. / Devedjiev, Y. / Derewenda, Z. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: The binding of the PDZ tandem of syntenin to target proteins Authors: Grembecka, J. / Cierpicki, T. / Devedjiev, Y. / Derewenda, U. / Kang, B.S. / Bushweller, J.H. / Derewenda, Z.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ybo.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ybo.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ybo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ybo_validation.pdf.gz | 451.5 KB | Display | wwPDB validaton report |
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Full document | 1ybo_full_validation.pdf.gz | 455.4 KB | Display | |
Data in XML | 1ybo_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1ybo_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/1ybo ftp://data.pdbj.org/pub/pdb/validation_reports/yb/1ybo | HTTPS FTP |
-Related structure data
Related structure data | 1v1tC 1w9eC 1w9oC 1w9qC 1n99S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The dimer in the assymetric unit is the biological assembly |
-Components
#1: Protein | Mass: 18018.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SDCBP, MDA9, SYCL / Plasmid: pGST-parallel-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O00560 #2: Protein/peptide | Mass: 1972.329 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: synthesized peptide cooresponding to the C-terminus of syndecan References: UniProt: P31431 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 49.7 % |
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Crystal grow | Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 0.2M NH4Cl, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 23083 / % possible obs: 99 % / Redundancy: 8.3 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.388 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 8.31 / Num. unique all: 2282 / Χ2: 1.208 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N99 Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.868 / SU B: 14.26 / SU ML: 0.189 / SU R Cruickshank DPI: 0.403 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.28 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.247 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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