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Yorodumi- PDB-3qdz: Crystal structure of the human thrombin mutant D102N in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qdz | ||||||
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Title | Crystal structure of the human thrombin mutant D102N in complex with the extracellular fragment of human PAR4. | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE RECEPTOR / Serine protease / protein function / protease-activated receptors / HYDROLASE-HYDROLASE RECEPTOR complex | ||||||
Function / homology | Function and homology information thrombin-activated receptor activity / platelet dense granule organization / positive regulation of Rho protein signal transduction / 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 / regulation of blood coagulation ...thrombin-activated receptor activity / platelet dense granule organization / positive regulation of Rho protein signal transduction / 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 / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / 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 / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / G protein-coupled receptor activity / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / platelet aggregation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / positive regulation of cell growth / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of cell shape / G alpha (q) signalling events / protease binding / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Gandhi, P. / Chen, Z. / Appelbaum, E. / Zapata, F. / Di Cera, E. | ||||||
Citation | Journal: IUBMB LIFE / Year: 2011 Title: Structural basis of thrombin-protease-receptor interactions Authors: Gandhi, P.S. / Chen, Z. / Appelbaum, E. / Zapata, F. / Di Cera, E. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Molecular dissection of Na+ binding to thrombin. Authors: Pineda, A.O. / Carrell, C.J. / Bush, L.A. / Prasad, S. / Caccia, S. / Chen, Z.W. / Mathews, F.S. / Di Cera, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qdz.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qdz.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 3qdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qdz_validation.pdf.gz | 467 KB | Display | wwPDB validaton report |
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Full document | 3qdz_full_validation.pdf.gz | 515.5 KB | Display | |
Data in XML | 3qdz_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 3qdz_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/3qdz ftp://data.pdbj.org/pub/pdb/validation_reports/qd/3qdz | HTTPS FTP |
-Related structure data
Related structure data | 1shhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3647.075 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell line (production host): BHK / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P00734, thrombin #2: Protein | Mass: 29779.234 Da / Num. of mol.: 2 / Mutation: D102N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell line (production host): BHK / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P00734, thrombin #3: Protein/peptide | Mass: 952.128 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2RL3, PAR4 / Cell line (production host): BHK / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q96RI0 |
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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: 2.51 Å3/Da / Density % sol: 50.98 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6 M tri-sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: APS 14-BM-C / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→40 Å / Num. all: 17276 / Num. obs: 16395 / % possible obs: 94.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 6.5 % / Biso Wilson estimate: 50.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 19.6 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1SHH Resolution: 2.8→40 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
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