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Yorodumi- PDB-3gis: Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gis | ||||||
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Title | Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin | ||||||
Components |
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Keywords | BLOOD CLOTTING / protein-protein complex / coagulation / Acute phase / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Gamma-carboxyglutamic acid / Glycoprotein / Hydrolase / Kringle / Protease / Secreted / Serine protease / Zymogen / EGF-like domain / Hydroxylation / Membrane / Receptor / Thrombophilia / Transmembrane | ||||||
Function / homology | Function and homology information blood coagulation, common pathway / negative regulation of blood coagulation / apicolateral plasma membrane / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity ...blood coagulation, common pathway / negative regulation of blood coagulation / apicolateral plasma membrane / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / response to X-ray / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / response to cAMP / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / female pregnancy / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / transmembrane signaling receptor activity / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor activity / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / response to lipopolysaccharide / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Adams, T.E. / Huntington, J.A. | ||||||
Citation | Journal: J.Thromb.Haemost. / Year: 2009 Title: Molecular basis of thrombomodulin activation of slow thrombin Authors: Adams, T.E. / Li, W. / Huntington, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gis.cif.gz | 266.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gis.ent.gz | 211.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/3gis ftp://data.pdbj.org/pub/pdb/validation_reports/gi/3gis | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein/peptide , 1 types, 3 molecules ACE
#1: Protein/peptide | Mass: 5641.175 Da / Num. of mol.: 3 / Fragment: Thrombin light-chain, UNP residues 315-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3)pLysS / References: UniProt: P00734, thrombin |
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-Protein , 2 types, 6 molecules BDFXYZ
#2: Protein | Mass: 29764.219 Da / Num. of mol.: 3 / Fragment: Thrombin heavy-chain, UNP residues 364-622 / Mutation: S195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3)pLysS / References: UniProt: P00734, thrombin #3: Protein | Mass: 12931.283 Da / Num. of mol.: 3 Fragment: Thrombomodulin EGF domains 4-5-6, UNP residues 363-483 Mutation: M388L,R456G,H457Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THBD, THRM / Plasmid: pET39b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07204 |
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-Non-polymers , 3 types, 593 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: 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: 2.63 Å3/Da / Density % sol: 53.19 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7 Details: 0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→91.9 Å / Num. all: 60765 / Num. obs: 58334 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.5 / % possible all: 95 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JOU, 1DX5 Resolution: 2.4→40 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 21.479 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.81 Å2 / Biso mean: 28.213 Å2 / Biso min: 2.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
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Refine LS restraints |
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Xplor file |
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