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Yorodumi- PDB-1m10: Crystal structure of the complex of Glycoprotein Ib alpha and the... -
+Open data
-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 | ||||||
Components |
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Keywords | BLOOD CLOTTING / leucine-rich repeat / HEMOSTASIS / DINUCLEOTIDE BINDING FOLD | ||||||
Function / homology | Function and homology information thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Weibel-Palade body / Defective F8 binding to von Willebrand factor / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / hemostasis / Defective F9 activation / Platelet Adhesion to exposed collagen / platelet alpha granule ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Weibel-Palade body / Defective F8 binding to von Willebrand factor / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / hemostasis / Defective F9 activation / Platelet Adhesion to exposed collagen / platelet alpha granule / 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 / immunoglobulin binding / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / 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 / extracellular matrix / Integrin signaling / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Huizinga, E.G. / Tsuji, S. / Romijn, R.A.P. / Schiphorst, M.E. / de Groot, P.G. / Sixma, J.J. / Gros, P. | ||||||
Citation | Journal: Science / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m10.cif.gz | 103.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m10.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 1m10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/1m10 ftp://data.pdbj.org/pub/pdb/validation_reports/m1/1m10 | HTTPS FTP |
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-Related structure data
Related structure data | 1m0zSC 1auqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: VWF / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P04275 |
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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.) Homo sapiens (human) / Gene: GP1BA / Plasmid: pCDNA3.1 / Production host: Mesocricetus auratus (golden hamster) / Tissue (production host): kidney / References: UniProt: P07359 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8075 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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