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Yorodumi- PDB-1u0n: The ternary von Willebrand Factor A1-glycoprotein Ibalpha-botroce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u0n | ||||||
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Title | The ternary von Willebrand Factor A1-glycoprotein Ibalpha-botrocetin complex | ||||||
Components |
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Keywords | BLOOD CLOTTING / Rossmann fold / LRR motif / C-type lectin fold / Protein-Protein complex | ||||||
Function / homology | Function and homology information thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective VWF binding to collagen type I / 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 / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective VWF binding to collagen type I / 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 / blood coagulation, intrinsic pathway / hemostasis / 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 / toxin activity / 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) Bothrops jararaca (jararaca) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Fukuda, K. / Liddington, R.C. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2005 Title: The snake venom protein botrocetin acts as a biological brace to promote dysfunctional platelet aggregation Authors: Fukuda, K. / Doggett, T. / Laurenzi, I.J. / Liddington, R.C. / Diacovo, T.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u0n.cif.gz | 152.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u0n.ent.gz | 124.1 KB | Display | PDB format |
PDBx/mmJSON format | 1u0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/1u0n ftp://data.pdbj.org/pub/pdb/validation_reports/u0/1u0n | HTTPS FTP |
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-Related 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: 23760.512 Da / Num. of mol.: 1 / Fragment: VWFA 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VWF,F8VWF / Production host: Escherichia coli (E. coli) / References: UniProt: P04275 |
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#2: Protein | Mass: 15233.202 Da / Num. of mol.: 1 / Fragment: Alpha chain / Source method: isolated from a natural source / Source: (natural) Bothrops jararaca (jararaca) / Secretion: venom / References: UniProt: P22029 |
#3: Protein | Mass: 15050.676 Da / Num. of mol.: 1 / Fragment: Beta chain / Source method: isolated from a natural source / Source: (natural) Bothrops jararaca (jararaca) / Secretion: venom / References: UniProt: P22030 |
#4: Protein | Mass: 29487.025 Da / Num. of mol.: 1 / Fragment: Alpha chain / Mutation: N21Q,N159Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GP1BA / Plasmid: pFASTBAC1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / 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: 3.9 Å3/Da / Density % sol: 68.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 3, 2003 |
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: 2.95→200 Å / Num. all: 28685 / Num. obs: 27144 / % possible obs: 94.6 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.099 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.95→3 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.1 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 171879.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 119.465 Å2 / ksol: 0.808019 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.95→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.11 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |