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- PDB-4c2b: Crystal Structure of High-Affinity von Willebrand Factor A1 domai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c2b | ||||||
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Title | Crystal Structure of High-Affinity von Willebrand Factor A1 domain with Disulfide Mutation in Complex with High Affinity GPIb alpha | ||||||
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![]() | BLOOD CLOTTING | ||||||
Function / homology | ![]() thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / 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 / positive regulation of leukocyte tethering or rolling ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / 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 / positive regulation of leukocyte tethering or rolling / hemostasis / blood coagulation, intrinsic pathway / Defective F9 activation / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / positive regulation of intracellular signal transduction / megakaryocyte development / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / regulation of blood coagulation / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / release of sequestered calcium ion into cytosol / fibrinolysis / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / cell morphogenesis / 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 surface receptor signaling pathway / cell adhesion / external side of plasma membrane / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Blenner, M.A. / Dong, X. / Springer, T.A. | ||||||
![]() | ![]() Title: Towards the Structural Basis of Regulation of Von Willebrand Factor Binding to Glycoprotein Ib Authors: Blenner, M.A. / Dong, X. / Springer, T.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 736.4 KB | Display | ![]() |
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PDB format | ![]() | 621.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 514 KB | Display | ![]() |
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Full document | ![]() | 530.4 KB | Display | |
Data in XML | ![]() | 62.9 KB | Display | |
Data in CIF | ![]() | 83.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c29C ![]() 4c2aSC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 24706.678 Da / Num. of mol.: 4 / Fragment: 1264-1468 / Mutation: YES Source method: isolated from a genetically manipulated source Details: HIGH AFFINITY MUTANT OF A1 / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 32492.104 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Details: HIGH AFFINITY MUTANT OF GPIB ALPHA WITH MUTATIONS TO REMOVE N-LINKED GLYCOSYLATION SITES, AND TWO PLATELET TYPE VWD MUTATIONS. Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 4 types, 77 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MES / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.23 % Description: THE RESOLUTION FOR A1 SS-GPIBALPHA-VWD2 WAS FOUND TO EXTEND TO 2.8 ANGSTROMS USING CROSS-CORRELATION. |
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Crystal grow | pH: 4.6 Details: CRYSTALS OF A1/SS-GPIB/VWD2 COMPLEX APPEARED IN DROPS WITH 20% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. THESE CRYSTALS WERE CRUSHED AND USED FOR ...Details: CRYSTALS OF A1/SS-GPIB/VWD2 COMPLEX APPEARED IN DROPS WITH 20% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. THESE CRYSTALS WERE CRUSHED AND USED FOR SEEDING CRYSTAL GROWTH IN 8 MG/ML COMPLEX, 15% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08 M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. SINCE THESE CRYSTALS WERE FORMED IN BUFFER CONTAINING 20% GLYCEROL, NO ADDITIONAL CRYOPROTECTION WAS USED. |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MX-300 / Detector: CCD / Date: Apr 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.48 |
Reflection | Resolution: 2.8→48.3 Å / Num. obs: 56526 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.59 / Net I/σ(I): 2.56 |
Reflection shell | Resolution: 2.8→2.87 Å / Mean I/σ(I) obs: 0.3 / % possible all: 80.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4C2A Resolution: 2.8→48.265 Å / SU ML: 0 / σ(F): 2 / Phase error: 27.94 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.265 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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