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Yorodumi- PDB-1ijk: The von Willebrand Factor mutant (I546V) A1 domain-botrocetin Complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ijk | ||||||
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Title | The von Willebrand Factor mutant (I546V) A1 domain-botrocetin Complex | ||||||
Components |
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Keywords | BLOOD CLOTTING/TOXIN / Dinucleotide-binding fold / C-type lectin fold / BLOOD CLOTTING-TOXIN COMPLEX | ||||||
Function / homology | Function and homology information 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 / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...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 / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / 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 adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Bothrops jararaca (jararaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Fukuda, K. / Doggett, T.A. / Bankston, L.A. / Cruz, M.A. / Diacovo, T.G. / Liddington, R.C. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structural basis of von Willebrand factor activation by the snake toxin botrocetin. Authors: Fukuda, K. / Doggett, T.A. / Bankston, L.A. / Cruz, M.A. / Diacovo, T.G. / Liddington, R.C. #1: Journal: J.Biol.Chem. / Year: 1998 Title: Crystal structure of the von Willebrand factor A1 domain and implications for the binding of platelet glycoprotein Ib Authors: Emsley, J. / Cruz, M. / Handin, R. / Liddington, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ijk.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ijk.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ijk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/1ijk ftp://data.pdbj.org/pub/pdb/validation_reports/ij/1ijk | 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: 23125.789 Da / Num. of mol.: 1 / Fragment: A1 domain / Mutation: I546V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04275 |
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#2: Protein | Mass: 15233.202 Da / Num. of mol.: 1 / Fragment: a-subunit / 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: b-subunit / Source method: isolated from a natural source / Source: (natural) Bothrops jararaca (jararaca) / Secretion: venom / References: UniProt: P22030 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.6 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 111 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.989 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.989 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. all: 18716 / Num. obs: 18178 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.207 / % possible all: 62.5 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 49341 |
Reflection shell | *PLUS % possible obs: 62.5 % / Num. unique obs: 594 / Mean I/σ(I) obs: 5.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→6 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1281188.06 / Data cutoff high rms absF: 1281188.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 94.79 Å2 / ksol: 0.9 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.66 Å / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 6 Å / Num. reflection obs: 14512 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.6 Å |