+Open data
-Basic information
Entry | Database: PDB / ID: 1atz | ||||||
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Title | HUMAN VON WILLEBRAND FACTOR A3 DOMAIN | ||||||
Components | VON WILLEBRAND FACTOR | ||||||
Keywords | COLLAGEN-BINDING / HEMOSTASIS / DINUCLEOTIDE BINDING FOLD | ||||||
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 / 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 / integrin binding / 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 / Platelet degranulation / protein-folding chaperone binding / protease binding / collagen-containing extracellular matrix / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Huizinga, E.G. / Gros, P. | ||||||
Citation | Journal: Structure / Year: 1997 Title: Crystal structure of the A3 domain of human von Willebrand factor: implications for collagen binding. Authors: Huizinga, E.G. / Martijn van der Plas, R. / Kroon, J. / 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 | 1atz.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1atz.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 1atz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1atz_validation.pdf.gz | 416.2 KB | Display | wwPDB validaton report |
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Full document | 1atz_full_validation.pdf.gz | 418.9 KB | Display | |
Data in XML | 1atz_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 1atz_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/1atz ftp://data.pdbj.org/pub/pdb/validation_reports/at/1atz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.999455, 0.028447, -0.016722), Vector: |
-Components
#1: Protein | Mass: 20151.979 Da / Num. of mol.: 2 / Fragment: A3-DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: B834 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P04275 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 34 % Description: 1.8 A IS THE HIGH RESOLUTION LIMIT OF THE DATA USED FOR REFINEMENT, NOT THE DIFFRACTION LIMIT OF THE CRYSTAL. | ||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 24% PEG 3000, 200 MM SODIUM ACETATE, 100 MM TRIS/HCL PH 8.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used to seeding | ||||||||||||||||||||
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: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 28127 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 43.8 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.059 / Mean I/σ(I) obs: 29.9 / Rsym value: 0.059 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→8 Å / Rfactor Rfree error: 0.0052 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 12.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.22 |