[English] 日本語
![](img/lk-miru.gif)
- PDB-1oak: CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR (VWF) A1 DOMAIN IN... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1oak | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR (VWF) A1 DOMAIN IN COMPLEX WITH THE FUNCTION BLOCKING NMC-4 FAB | ||||||
![]() |
| ||||||
![]() | COMPLEX (WILLEBRAND/IMMUNOGLOBULIN) / VON WILLEBRAND FACTOR / GLYCOPROTEIN IBA (A:ALPHA) BINDING / COMPLEX (WILLEBRAND-IMMUNOGLOBULIN) / BLOOD COAGULATION / COMPLEX (WILLEBRAND-IMMUNOGLOBULIN) complex | ||||||
Function / homology | ![]() 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 / humoral immune response mediated by circulating immunoglobulin / platelet alpha granule ...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 / humoral immune response mediated by circulating immunoglobulin / platelet alpha granule / phagocytosis, recognition / Platelet Adhesion to exposed collagen / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / phagocytosis, engulfment / 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 / immunoglobulin mediated immune response / Integrin cell surface interactions / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / B cell differentiation / 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 / positive regulation of immune response / 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 / defense response to bacterium / external side of plasma membrane / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Celikel, R. / Varughese, K.I. | ||||||
![]() | ![]() Title: Crystal structure of the von Willebrand factor A1 domain in complex with the function blocking NMC-4 Fab. Authors: Celikel, R. / Varughese, K.I. / Madhusudan / Yoshioka, A. / Ware, J. / Ruggeri, Z.M. #1: ![]() Title: Crystal Structure of Nmc-4 Fab Anti-Von Willebrand Factor A1 Domain Authors: Celikel, R. / Madhusudan / Varughese, K.I. / Shima, M. / Yoshioka, A. / Ware, J. / Ruggeri, Z.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 138.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 112.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 378 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 394.8 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Antibody | Mass: 23461.805 Da / Num. of mol.: 1 Fragment: FAB FRAGMENT, AN ANTI VON WILLEBRAND FACTOR (VWF) A1 DOMAIN Source method: isolated from a genetically manipulated source Details: THE ANTIBODY HEAVY CHAIN CONSISTS OF TWO SEGMENTS, H1 AND H2, BOTH LABELED CHAIN H IN THIS ENTRY Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Antibody | Mass: 23887.551 Da / Num. of mol.: 1 Fragment: FAB FRAGMENT, AN ANTI VON WILLEBRAND FACTOR (VWF) A1 DOMAIN Source method: isolated from a genetically manipulated source Details: THE ANTIBODY HEAVY CHAIN CONSISTS OF TWO SEGMENTS, H1 AND H2, BOTH LABELED CHAIN H IN THIS ENTRY Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 22444.135 Da / Num. of mol.: 1 Fragment: A1 DOMAIN RESIDUES 507 - 702, OR GLYCOPROTEIN IBA (A\:ALPHA) BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 64 % |
---|---|
Crystal grow | pH: 8 / Details: pH 8 |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: PT COATED SI FLAT MIRROR BENT FOR VERTICAL FOCUS |
Radiation | Monochromator: BENT CYLINDRICAL GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 44346 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.048 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 6.4 / % possible all: 98.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() ![]() Starting model: NMC4 (FAB) Resolution: 2.2→50 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|