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Yorodumi- PDB-1fe8: CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR A3 DOMAIN IN COMPL... -
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-Basic information
Entry | Database: PDB / ID: 1fe8 | |||||||||
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Title | CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR A3 DOMAIN IN COMPLEX WITH A FAB FRAGMENT OF IGG RU5 THAT INHIBITS COLLAGEN BINDING | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Collagen binding / conformational changes / epitope / von Willebrand factor A-type domain | |||||||||
Function / homology | Function and homology information 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 / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...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 / 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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / complement activation, classical pathway / antigen binding / 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 / antibacterial humoral response / collagen-containing extracellular matrix / protease binding / blood microparticle / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å | |||||||||
Authors | Bouma, B. / Huizinga, E.G. / Schiphorst, M.E. / Sixma, J.J. / Kroon, J. / Gros, P. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Identification of the collagen-binding site of the von Willebrand factor A3-domain. Authors: Romijn, R.A. / Bouma, B. / Wuyster, W. / Gros, P. / Kroon, J. / Sixma, J.J. / Huizinga, E.G. #1: Journal: Structure / Year: 1997 Title: Crystal structure of the A3 domain of human von Willebrand factor: implications for collagen binding Authors: Huizinga, E.G. / van der Plas, R.M. / Kroon, J. / Sixma, J.J. / Gros, P. #2: Journal: To be Published Title: Binding of von Willebrand Factor to collagen type III: role of specific amino acids in the collagen binding domain and effects of neighbouring domains Authors: van der Plas, R.M. / Gomes, L. / Marquart, J.A. / Vink, T. / Meijers, J.C.M. / de Groot, P.G. / Sixma, J.J. / Huizinga, E.G. #3: Journal: J.Biol.Chem. / Year: 1997 Title: The von Willebrand Factor A3 domain does not contain a metal ion-dependent adhesion site motif Authors: Bienkowska, J. / Cruz, M. / Atiemo, A. / 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 | 1fe8.cif.gz | 367.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fe8.ent.gz | 300.6 KB | Display | PDB format |
PDBx/mmJSON format | 1fe8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fe8_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1fe8_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1fe8_validation.xml.gz | 77.6 KB | Display | |
Data in CIF | 1fe8_validation.cif.gz | 109 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/1fe8 ftp://data.pdbj.org/pub/pdb/validation_reports/fe/1fe8 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 21025.176 Da / Num. of mol.: 3 / Fragment: COLLAGEN BINDING DOMAIN A3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P04275 |
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-Antibody , 2 types, 6 molecules HIJLMN
#2: Antibody | Mass: 22420.012 Da / Num. of mol.: 3 / Fragment: FAB FRAGMENT HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01863*PLUS #3: Antibody | Mass: 23192.434 Da / Num. of mol.: 3 / Fragment: FAB FRAGMENT LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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-Sugars , 2 types, 5 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 2 types, 879 molecules
#6: Chemical | ChemComp-CAC / |
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#7: 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: 3.31 Å3/Da / Density % sol: 62.79 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: iso-propanol, MPD, cacodylate, sodium chloride, Tris , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.3 | ||||||||||||||||||||||||||||||
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: BW7B / Wavelength: 0.8469 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8469 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→29.9 Å / Num. all: 143255 / Num. obs: 143245 / % possible obs: 85.9 % / Observed criterion σ(I): -3.5 / Redundancy: 4.2 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.404 / Num. unique all: 8424 / % possible all: 51.5 |
Reflection | *PLUS Num. obs: 143255 |
Reflection shell | *PLUS % possible obs: 51.5 % / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Resolution: 2.03→29.9 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: used maximum likelihood refinement against structure factors
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Refinement step | Cycle: LAST / Resolution: 2.03→29.9 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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