+Open data
-Basic information
Entry | Database: PDB / ID: 6c2w | |||||||||
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Title | Crystal structure of human prothrombin mutant S101C/A470C | |||||||||
Components | Prothrombin | |||||||||
Keywords | BLOOD CLOTTING / Hydrolase / Kringle / enzyme mechanism / coagulation factor | |||||||||
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 / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / 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 / 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 / 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 / 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 / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / 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 / 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) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.12 Å | |||||||||
Authors | Chinnaraj, M. / Chen, Z. / Pelc, L. / Grese, Z. / Bystranowska, D. / Di Cera, E. / Pozzi, N. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2018 Title: Structure of prothrombin in the closed form reveals new details on the mechanism of activation. Authors: Chinnaraj, M. / Chen, Z. / Pelc, L.A. / Grese, Z. / Bystranowska, D. / Di Cera, E. / Pozzi, N. #1: Journal: J. Biol. Chem. / Year: 2016 Title: How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin. Authors: Pozzi, N. / Chen, Z. / 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 | 6c2w.cif.gz | 245 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c2w.ent.gz | 195.9 KB | Display | PDB format |
PDBx/mmJSON format | 6c2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/6c2w ftp://data.pdbj.org/pub/pdb/validation_reports/c2/6c2w | HTTPS FTP |
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-Related structure data
Related structure data | 6bjrC 3nxpS 5edmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 66309.875 Da / Num. of mol.: 2 / Mutation: S101C, A470C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell line (production host): Baby Hamster Kidney / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P00734, thrombin #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-MG / #4: Sugar | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 9 / Details: 100 mM Bicine, pH 9.0 and 11% PEG 3350 |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 17, 2017 | |||||||||||||||||||||||||
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 4.1→40 Å / Num. obs: 30018 / % possible obs: 91.7 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 5.7 | |||||||||||||||||||||||||
Reflection shell | Resolution: 4.1→4.17 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.675 / Num. unique obs: 1219 / % possible all: 74.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EDM and 3NXP Resolution: 4.12→30.32 Å / Cor.coef. Fo:Fc: 0.827 / Cor.coef. Fo:Fc free: 0.74 / SU B: 19.344 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 191.324 Å2
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Refinement step | Cycle: 1 / Resolution: 4.12→30.32 Å
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