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Yorodumi- PDB-2ouh: Crystal structure of the Thrombospondin-1 N-terminal domain in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ouh | ||||||
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Title | Crystal structure of the Thrombospondin-1 N-terminal domain in complex with fractionated Heparin DP10 | ||||||
Components | Thrombospondin-1 | ||||||
Keywords | CELL ADHESION / TSP-1 / TSPN-1 / HBD / Fractionated Heparin / DP10 | ||||||
Function / homology | Function and homology information negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / negative regulation of dendritic cell antigen processing and presentation / negative regulation of nitric oxide mediated signal transduction / negative regulation of sprouting angiogenesis / chronic inflammatory response / negative regulation of endothelial cell chemotaxis / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins ...negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / negative regulation of dendritic cell antigen processing and presentation / negative regulation of nitric oxide mediated signal transduction / negative regulation of sprouting angiogenesis / chronic inflammatory response / negative regulation of endothelial cell chemotaxis / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of long-chain fatty acid import across plasma membrane / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of transforming growth factor beta1 production / engulfment of apoptotic cell / negative regulation of focal adhesion assembly / low-density lipoprotein particle binding / fibrinogen complex / peptide cross-linking / fibrinogen binding / Signaling by PDGF / positive regulation of chemotaxis / platelet alpha granule / negative regulation of interleukin-12 production / positive regulation of endothelial cell apoptotic process / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of plasminogen activation / transforming growth factor beta binding / positive regulation of macrophage activation / positive regulation of fibroblast migration / negative regulation of blood vessel endothelial cell migration / sprouting angiogenesis / proteoglycan binding / negative regulation of endothelial cell migration / extracellular matrix structural constituent / Syndecan interactions / endopeptidase inhibitor activity / negative regulation of cell-matrix adhesion / negative regulation of cGMP-mediated signaling / positive regulation of macrophage chemotaxis / response to testosterone / fibroblast growth factor binding / phosphatidylserine binding / positive regulation of transforming growth factor beta receptor signaling pathway / behavioral response to pain / negative regulation of endothelial cell proliferation / positive regulation of phosphorylation / response to magnesium ion / fibronectin binding / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / Integrin cell surface interactions / positive regulation of blood coagulation / negative regulation of fibrinolysis / response to glucose / negative regulation of angiogenesis / response to mechanical stimulus / laminin binding / nitric oxide-cGMP-mediated signaling / positive regulation of endothelial cell migration / response to endoplasmic reticulum stress / extracellular matrix / positive regulation of smooth muscle cell proliferation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of MAP kinase activity / platelet alpha granule lumen / sarcoplasmic reticulum / secretory granule / response to progesterone / positive regulation of translation / negative regulation of extrinsic apoptotic signaling pathway / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / response to calcium ion / cellular response to growth factor stimulus / integrin binding / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / positive regulation of tumor necrosis factor production / cell migration / Platelet degranulation / cellular response to tumor necrosis factor / heparin binding / cellular response to heat / protease binding / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia / cell adhesion / positive regulation of cell migration / response to xenobiotic stimulus / inflammatory response / immune response / negative regulation of cell population proliferation / endoplasmic reticulum lumen / external side of plasma membrane / positive regulation of cell population proliferation / calcium ion binding / negative regulation of apoptotic process / apoptotic process / cell surface Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Tan, K. / Joachimiak, A. / Wang, J. / Lawler, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Heparin-induced cis- and trans-Dimerization Modes of the Thrombospondin-1 N-terminal Domain. Authors: Tan, K. / Duquette, M. / Liu, J.H. / Shanmugasundaram, K. / Joachimiak, A. / Gallagher, J.T. / Rigby, A.C. / Wang, J.H. / Lawler, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ouh.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ouh.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ouh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ouh_validation.pdf.gz | 453.4 KB | Display | wwPDB validaton report |
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Full document | 2ouh_full_validation.pdf.gz | 462.3 KB | Display | |
Data in XML | 2ouh_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 2ouh_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/2ouh ftp://data.pdbj.org/pub/pdb/validation_reports/ou/2ouh | HTTPS FTP |
-Related structure data
Related structure data | 2es3C 2oujC 1z78S 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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2 |
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Unit cell |
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Details | TSPN-1 is a monomer by itself. In presence of DP10, it forms a heparin-linked dimer. |
-Components
#1: Protein | Mass: 27556.102 Da / Num. of mol.: 2 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THBS1, TSP, TSP1 / Plasmid: PMT/BIP/V5-HIS A / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): DROSOPHILA S2 CELL / References: UniProt: P07996 #2: Chemical | ChemComp-SO4 / #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: 1.82 Å3/Da / Density % sol: 32.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% PEG1500, 0.08M Sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.99187 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2004 / Details: Mirror |
Radiation | Monochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. all: 14771 / Num. obs: 14771 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 29.87 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.63 / Num. unique all: 1048 / % possible all: 65.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Z78 Resolution: 2.4→100 Å / σ(F): 0 / σ(I): 0 Details: Fractionated heparin DP10 is chemically heterogeneous and partially disordered in the structure. Authors were able to identify only some SO4 groups from the heparin but not the heparin ...Details: Fractionated heparin DP10 is chemically heterogeneous and partially disordered in the structure. Authors were able to identify only some SO4 groups from the heparin but not the heparin backbone due to its possible mobility. Instead, there are several water molecules being positioned into some uncharacterized densities near heparin binding sites. These densities are likely from partially disordered heparin dp10, not necessarily from water molecules. Including of these waters in the model was just for the refinement purposes.
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Refinement step | Cycle: LAST / Resolution: 2.4→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.48 Å /
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