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- PDB-3hxq: Crystal Structure of Von Willebrand Factor (VWF) A1 Domain in Com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hxq | ||||||
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Title | Crystal Structure of Von Willebrand Factor (VWF) A1 Domain in Complex with DNA Aptamer ARC1172, an Inhibitor of VWF-Platelet Binding | ||||||
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![]() | BLOOD CLOTTING/BLOOD CLOTTING REGULATOR / ARC1779 / VWF / Platelet Glycoprotein Ib / Aptamer / ARC1772 / Blood coagulation / Cell adhesion / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Extracellular matrix / Glycoprotein / Hemostasis / Isopeptide bond / Secreted / von Willebrand disease / BLOOD CLOTTING-BLOOD CLOTTING REGULATOR COMPLEX | ||||||
Function / homology | ![]() Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Huang, R.H. / Sadler, J.E. / Fremont, D.H. / Diener, J.L. / Schaub, R.G. | ||||||
![]() | ![]() Title: A structural explanation for the antithrombotic activity of ARC1172, a DNA aptamer that binds von Willebrand factor domain A1. Authors: Huang, R.H. / Fremont, D.H. / Diener, J.L. / Schaub, R.G. / Sadler, J.E. #1: Journal: Circulation / Year: 2007 Title: First-in-human evaluation of anti von Willebrand factor therapeutic aptamer ARC1779 in healthy volunteers. Authors: Gilbert, J.C. / DeFeo-Fraulini, T. / Hutabarat, R.M. / Horvath, C.J. / Merlino, P.G. / Marsh, H.N. / Healy, J.M. / Boufakhreddine, S. / Holohan, T.V. / Schaub, R.G. #2: Journal: J.Thromb.Haemost. / Year: 2009 Title: Inhibition of von Willebrand factor-mediated platelet activation and thrombosis by the anti-von Willebrand factor A1-domain aptamer ARC1779. Authors: Diener, J.L. / Daniel Lagasse, H.A. / Duerschmied, D. / Merhi, Y. / Tanguay, J.F. / Hutabarat, R. / Gilbert, J. / Wagner, D.D. / Schaub, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.6 KB | Display | ![]() |
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PDB format | ![]() | 113.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430 KB | Display | ![]() |
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Full document | ![]() | 437.5 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hxoSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 23889.627 Da / Num. of mol.: 1 Fragment: von Willebrand factor (VWF) A1 Domain (residues 1260-1468) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 12884.188 Da / Num. of mol.: 1 / Fragment: Aptamer ARC1172 / Source method: obtained synthetically Details: ARC1172 is a DNA oligonucleotides that bind specific target molecules, identified by selection in vitro from large random sequence libraries (termed SELEX: systematic evolution of ligands by ...Details: ARC1172 is a DNA oligonucleotides that bind specific target molecules, identified by selection in vitro from large random sequence libraries (termed SELEX: systematic evolution of ligands by exponential enrichment) |
#3: Water | ChemComp-HOH / |
Compound details | AUTHOR STATE THAT THE LAST RESIDUE OF THE DNA POLYMER IS AN INVERTED-DT WHICH IS NOT MODELED DUE TO ...AUTHOR STATE THAT THE LAST RESIDUE OF THE DNA POLYMER IS AN INVERTED-DT WHICH IS NOT MODELED DUE TO DISORDER. 3' INVERTED DT IS LINKED TO THE PHOSPHATE GROUP OF ITS PREVIOUS RESIDUE BY THE THIRD CARBON ATOMS OF THE SUGAR RINGS. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % |
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Crystal grow | Temperature: 293 K / pH: 4.6 Details: 0.2 M NH4Ac, 0.1 M NaAc, 30% PEG4000, pH 4.6, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 17, 2008 |
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: 2.694→38 Å / Num. obs: 9819 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.69→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.8 / % possible all: 83.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HXO Resolution: 2.694→38 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.44 / σ(F): 1.5 / Phase error: 27.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.193 Å2 / ksol: 0.311 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 170.21 Å2 / Biso mean: 63.419 Å2 / Biso min: 17.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.694→38 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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