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Yorodumi- PDB-1za4: Crystal Structure of the Thrombospondin-1 N-terminal Domain in Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1za4 | |||||||||
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Title | Crystal Structure of the Thrombospondin-1 N-terminal Domain in Complex with Arixtra | |||||||||
Components | Thrombospondin 1 | |||||||||
Keywords | CELL ADHESION / TSP-1 / NTSP-1 / HBD / ARIXTRA | |||||||||
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 / chronic inflammatory response / negative regulation of sprouting angiogenesis / 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 / chronic inflammatory response / negative regulation of sprouting angiogenesis / 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 / positive regulation of transforming growth factor beta1 production / 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 / engulfment of apoptotic cell / low-density lipoprotein particle binding / negative regulation of focal adhesion assembly / fibrinogen complex / peptide cross-linking / positive regulation of chemotaxis / fibrinogen binding / Signaling by PDGF / platelet alpha granule / negative regulation of interleukin-12 production / negative regulation of cell migration involved in sprouting angiogenesis / positive regulation of macrophage activation / negative regulation of plasminogen activation / transforming growth factor beta binding / positive regulation of endothelial cell apoptotic process / positive regulation of fibroblast 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 / phosphatidylserine binding / positive regulation of macrophage chemotaxis / negative regulation of cGMP-mediated signaling / response to testosterone / fibroblast growth factor binding / behavioral response to pain / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of endothelial cell proliferation / response to magnesium ion / negative regulation of blood vessel endothelial cell migration / fibronectin binding / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / Integrin cell surface interactions / laminin binding / positive regulation of blood coagulation / negative regulation of fibrinolysis / response to glucose / response to mechanical stimulus / positive regulation of phosphorylation / response to endoplasmic reticulum stress / negative regulation of angiogenesis / extracellular matrix / positive regulation of endothelial cell migration / positive regulation of translation / platelet alpha granule lumen / sarcoplasmic reticulum / response to progesterone / secretory granule / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of smooth muscle cell proliferation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of MAP kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to growth factor stimulus / response to calcium ion / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / cell migration / integrin binding / positive regulation of tumor necrosis factor production / Platelet degranulation / cellular response to heat / heparin binding / cellular response to tumor necrosis factor / collagen-containing extracellular matrix / protease binding / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of cell migration / immune response / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / external side of plasma membrane / endoplasmic reticulum lumen / apoptotic process / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / endoplasmic reticulum Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | |||||||||
Authors | Tan, K. / Wang, J.H. / Lawler, J. | |||||||||
Citation | Journal: Structure / Year: 2006 Title: The Structures of the Thrombospondin-1 N-terminal Domain and its Complex with a Synthetic Pentameric Heparin Authors: Tan, K. / Duquette, M. / Liu, J.H. / Zhang, R. / Joachimiak, A. / Wang, J.H. / Lawler, J. | |||||||||
History |
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Remark 600 | HETEROGEN ARIXTRA (FONDAPARINUX SODIUM) IS A SYNTHETIC MODIFIED PENTAMERIC HEPARIN. THE COMPLETE ...HETEROGEN ARIXTRA (FONDAPARINUX SODIUM) IS A SYNTHETIC MODIFIED PENTAMERIC HEPARIN. THE COMPLETE ARIXTRA MOLECULE WAS NOT OBSERVED. SGN, N,O6-DISULFO-GLUCOSAMINE IS PART OF ARIXTRA MOLECULE (DEFINED AS FIFTH UNIT) AND SO4, SULFATE IONS ARE ALSO PART OF ARIXTRA MOLECULE (FRAGMENTS FROM THE REST OF THE UNITS). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1za4.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1za4.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 1za4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/1za4 ftp://data.pdbj.org/pub/pdb/validation_reports/za/1za4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27649.893 Da / Num. of mol.: 1 / 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 / Genus (production host): Drosophila / Production host: Drosophila (fruit flies) / Strain (production host): Drosophila S2 cell / References: UniProt: P07996 | ||
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#2: Sugar | ChemComp-SGN / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% PEG1500 AND 0.1 M NAAC , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. obs: 30776 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 27.1 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 1.85 / Num. unique all: 2479 / % possible all: 78.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→25 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.2 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 3 Å / Luzzati sigma a obs: 0.15 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å
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