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- PDB-1p9a: Crystal Structure of N-Terminal Domain of Human Platelet Receptor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p9a | |||||||||
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Title | Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha at 1.7 Angstrom Resolution | |||||||||
![]() | Platelet glycoprotein Ib alpha chain precursor | |||||||||
![]() | BLOOD CLOTTING / Platelet Receptors / Glycocalicin / Leucine Rich Repeats | |||||||||
Function / homology | ![]() 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 / regulation of blood coagulation / Platelet Aggregation (Plug Formation) / release of sequestered calcium ion into cytosol / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / extracellular matrix / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell morphogenesis / platelet activation / blood coagulation / cell surface receptor signaling pathway / cell adhesion / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Varughese, K.I. / Celikel, R. / Ruggeri, Z.M. | |||||||||
![]() | ![]() Title: Modulation of alpha-thrombin function by distinct interactions with platelet glycoprotein Ibalpha Authors: Celikel, R. / McClintock, R.A. / Roberts, J.R. / Mendolicchio, G.L. / Ware, J. / Varughese, K.I. / Ruggeri, Z.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.2 KB | Display | ![]() |
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PDB format | ![]() | 48.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 734.6 KB | Display | ![]() |
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Full document | ![]() | 738.6 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 32306.787 Da / Num. of mol.: 1 / Fragment: N-Terminal Domain / Mutation: C65A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.89 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 6000, Sodium Nitrate, Sodium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2002 |
Radiation | Monochromator: Curved Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0642 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 31316 / Num. obs: 160737 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rsym value: 0.061 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 5.3 / Rsym value: 0.317 / % possible all: 73.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2.7 Angstrom P21/GPIb-alpha MAD structure-to be published Resolution: 1.7→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |