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Yorodumi- PDB-4ch2: Low-salt crystal structure of a thrombin-GpIbalpha peptide complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ch2 | ||||||
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Title | Low-salt crystal structure of a thrombin-GpIbalpha peptide complex | ||||||
Components |
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Keywords | HYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX | ||||||
Function / homology | Function and homology information thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling / 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 / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / extracellular matrix / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / growth factor activity / cell morphogenesis / 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 / positive regulation of cell growth / regulation of cell shape / 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 / cell adhesion / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Lechtenberg, B.C. / Freund, S.M.V. / Huntington, J.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Gpibalpha Interacts Exclusively with Exosite II of Thrombin Authors: Lechtenberg, B.C. / Freund, S.M.V. / 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 | 4ch2.cif.gz | 260.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ch2.ent.gz | 210.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ch2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ch2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4ch2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ch2_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 4ch2_validation.cif.gz | 44.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/4ch2 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/4ch2 | HTTPS FTP |
-Related structure data
Related structure data | 4ch8C 1ppbS 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
-Protein/peptide , 2 types, 4 molecules ACPQ
#1: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET23 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR, PLYSS / References: UniProt: P00734, thrombin #3: Protein/peptide | Mass: 1935.584 Da / Num. of mol.: 2 / Fragment: C-TERMINAL FRAGMENT OF GPIBALPHA, 271-284 / Source method: obtained synthetically / Details: ALL THREE TYROSINE RESIDUES ARE PHOSPHORYLATED / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P07359 |
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-Protein , 1 types, 2 molecules BD
#2: Protein | Mass: 29780.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET23 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR, PLYSS / References: UniProt: P00734, thrombin |
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-Non-polymers , 4 types, 481 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | DEOXY-CHLOROMETH |
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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: 2.15 Å3/Da / Density % sol: 42.82 % / Description: NONE |
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Crystal grow | pH: 7.4 / Details: 50 MM SODIUM FORMATE, 16% PEG-3350, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→41.2 Å / Num. obs: 72363 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.8 / % possible all: 98.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PPB Resolution: 1.6→37.1 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.027 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. DISORDERED REGIONS AND SIDE CHAINS ARE NOT MODELED.
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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: 16.614 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→37.1 Å
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Refine LS restraints |
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