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Yorodumi- PDB-4dii: X-ray structure of the complex between human alpha thrombin and t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dii | ||||||
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Title | X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of potassium ions | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR/DNA / protein-DNA complex / serine protease / blood coagulation / aptamer / hydrolase-hydrolase inhibitor-DNA complex / serine protease fold / DNA aptamer / blood / G-quadruplex | ||||||
Function / homology | Function and homology information 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 ...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 / 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 / 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 / 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 / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / 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 / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Synthetic DNA (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Russo Krauss, I. / Merlino, A. / Mazzarella, L. / Sica, F. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity. Authors: Russo Krauss, I. / Merlino, A. / Randazzo, A. / Novellino, E. / Mazzarella, L. / Sica, F. #1: Journal: Nucleic Acids Res. / Year: 2011 Title: Thrombin-aptamer recognition: a revealed ambiguity. Authors: Russo Krauss, I. / Merlino, A. / Giancola, C. / Randazzo, A. / Mazzarella, L. / Sica, F. #2: Journal: J.Biol.Chem. / Year: 1993 Title: The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer. Authors: Padmanabhan, K. / Padmanabhan, K.P. / Ferrara, J.D. / Sadler, J.E. / Tulinsky, A. #3: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: An ambiguous structure of a DNA 15-mer thrombin complex. Authors: Padmanabhan, K. / Tulinsky, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dii.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dii.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 4dii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/4dii ftp://data.pdbj.org/pub/pdb/validation_reports/di/4dii | HTTPS FTP |
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-Related structure data
Related structure data | 4dihC 1haoS 3qlpS C: citing same article (ref.) S: Starting model for refinement |
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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 | 1:1 protein-DNA aptamer complex |
-Components
-Protein/peptide / Protein / DNA chain / Sugars , 4 types, 4 molecules LHD
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: Light chain (UNP Residues 328-363) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
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#2: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: Heavy chain (UNP Residues 364-622) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin |
#3: DNA chain | Mass: 4743.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic DNA (others) |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 190 molecules
#4: Chemical | #5: Chemical | ChemComp-0G6 / | #7: Chemical | ChemComp-NA / | #8: Chemical | #9: Chemical | ChemComp-K / | #10: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE RESIDUES: 1) VIA A HEMIKETAL GROUP TO OG SER ...THE INHIBITOR IS COVALENTLY |
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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: 2.29 Å3/Da / Density % sol: 46.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 10-15% w/v polyethylene glycol 8000, 0.05 M zinc acetate, 0.1 M sodium cacodylate , pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 10, 2009 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 20850 / Num. obs: 20850 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.05→2.12 Å / % possible all: 84.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QLP AND 1HAO Resolution: 2.05→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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