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- PDB-1m10: Crystal structure of the complex of Glycoprotein Ib alpha and the... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m10 | ||||||
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Title | Crystal structure of the complex of Glycoprotein Ib alpha and the von Willebrand Factor A1 Domain | ||||||
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![]() | BLOOD CLOTTING / leucine-rich repeat / HEMOSTASIS / DINUCLEOTIDE BINDING FOLD | ||||||
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 / collagen binding / fibrinolysis / 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 / protease binding / collagen-containing extracellular matrix / 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 | ![]() ![]() ![]() | ||||||
![]() | Huizinga, E.G. / Tsuji, S. / Romijn, R.A.P. / Schiphorst, M.E. / de Groot, P.G. / Sixma, J.J. / Gros, P. | ||||||
![]() | ![]() Title: Structures of glycoprotein Ibalpha and its complex with von Willebrand factor A1 domain. Authors: Huizinga, E.G. / Tsuji, S. / Romijn, R.A. / Schiphorst, M.E. / de Groot, P.G. / Sixma, J.J. / Gros, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.2 KB | Display | ![]() |
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PDB format | ![]() | 79.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1m0zSC ![]() 1auqS 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
#1: Protein | Mass: 23731.447 Da / Num. of mol.: 1 / Fragment: A1 domain / Mutation: R543Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 32334.842 Da / Num. of mol.: 1 / Fragment: von Willebrand Factor binding domain / Mutation: N21Q N159Q M239V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.47 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 3000, sodium chloride, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: CCD / Date: Dec 12, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8075 Å / Relative weight: 1 |
Reflection | Resolution: 3.09→30.5 Å / Num. all: 10454 / Num. obs: 10454 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 5.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 3.09→3.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1037 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 40 Å |
Reflection shell | *PLUS Highest resolution: 3.1 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.48 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 1AUQ and 1M0Z Resolution: 3.1→30.5 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1123736.97 / Data cutoff low absF: 0 / Isotropic thermal model: ISOTROPIC RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.2789 Å2 / ksol: 0.300589 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→30.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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