+Open data
-Basic information
Entry | Database: PDB / ID: 1lsl | ||||||
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Title | Crystal Structure of the Thrombospondin-1 Type 1 Repeats | ||||||
Components | Thrombospondin 1 | ||||||
Keywords | CELL ADHESION / TSP-1 / TSR | ||||||
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 / Defective B3GALTL causes PpS / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / Defective B3GALTL causes PpS / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / negative regulation of plasminogen activation / positive regulation of macrophage activation / transforming growth factor beta binding / positive regulation of endothelial cell apoptotic process / negative regulation of endothelial cell migration / positive regulation of fibroblast migration / sprouting angiogenesis / proteoglycan binding / 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 / negative regulation of endothelial cell proliferation / response to testosterone / fibroblast growth factor binding / behavioral response to pain / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of blood vessel endothelial cell migration / response to magnesium ion / fibronectin binding / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / laminin binding / Integrin cell surface interactions / positive regulation of blood coagulation / negative regulation of fibrinolysis / response to glucose / response to mechanical stimulus / positive regulation of phosphorylation / extracellular matrix / response to endoplasmic reticulum stress / negative regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of translation / platelet alpha granule lumen / response to progesterone / sarcoplasmic reticulum / 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 / endoplasmic reticulum lumen / negative regulation of cell population proliferation / external side of plasma membrane / 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. / Duquette, M. / Liu, J. / Dong, Y. / Zhang, R. / Joachimiak, A. / Lawler, J. / Wang, J.-H. | ||||||
Citation | Journal: J.Cell Biol. / Year: 2002 Title: Crystal structure of the TSP-1 type 1 repeats: a novel layered fold and its biological implication. Authors: Tan, K. / Duquette, M. / Liu, J.H. / Dong, Y. / Zhang, R. / Joachimiak, A. / Lawler, J. / Wang, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lsl.cif.gz | 34.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lsl.ent.gz | 25.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lsl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/1lsl ftp://data.pdbj.org/pub/pdb/validation_reports/ls/1lsl | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12176.628 Da / Num. of mol.: 1 / Fragment: TSP Type 1 Repeats 2 and 3 (residues 434-546) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THBS1 / Plasmid: PMT-BIP-V5-HIS A / Genus (production host): Drosophila / Cell (production host): S2 cells / Production host: Drosophila (fruit flies) / References: UniProt: P07996 |
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#2: Sugar | ChemComp-FUL / |
#3: Sugar | ChemComp-FUC / |
#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: 3.56 Å3/Da / Density % sol: 65.2 % | ||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.5 M sodium potassium tartrate and 0.1 M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-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→20 Å / Num. obs: 15123 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.6 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 3.8 / % possible all: 99.7 | ||||||||||||||||||
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. obs: 15485 / Num. measured all: 162978 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 99.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 42.28 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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