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- PDB-5xjf: Crystal structure of fucosylated IgG Fc Y296W mutant complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xjf | |||||||||
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Title | Crystal structure of fucosylated IgG Fc Y296W mutant complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa | |||||||||
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![]() | IMMUNE SYSTEM / COMPLEX / FC FRAGMENT / IGG / RECEPTOR / CD16 / GAMMA | |||||||||
Function / homology | ![]() immune receptor activity / low-affinity IgG receptor activity / natural killer cell degranulation / IgG receptor activity / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / macrophage activation / natural killer cell mediated cytotoxicity / natural killer cell activation / positive regulation of natural killer cell proliferation ...immune receptor activity / low-affinity IgG receptor activity / natural killer cell degranulation / IgG receptor activity / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / macrophage activation / natural killer cell mediated cytotoxicity / natural killer cell activation / positive regulation of natural killer cell proliferation / antibody-dependent cellular cytotoxicity / IgG binding / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / complement activation, classical pathway / calcium-mediated signaling / FCGR3A-mediated phagocytosis / antigen binding / Regulation of actin dynamics for phagocytic cup formation / positive regulation of tumor necrosis factor production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / cell surface receptor signaling pathway / blood microparticle / immune response / external side of plasma membrane / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sakae, Y. / Satoh, T. / Yagi, H. / Yanaka, S. / Yamaguchi, T. / Isoda, Y. / Iida, S. / Okamoto, Y. / Kato, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fc gamma receptor IIIa. Authors: Sakae, Y. / Satoh, T. / Yagi, H. / Yanaka, S. / Yamaguchi, T. / Isoda, Y. / Iida, S. / Okamoto, Y. / Kato, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.2 KB | Display | ![]() |
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PDB format | ![]() | 109.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xjeC ![]() 3ay4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Antibody / Protein , 2 types, 3 molecules ABC
#1: Antibody | Mass: 25120.469 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 227-449 / Mutation: Y298W Source method: isolated from a genetically manipulated source Details: Fc fragment / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 20641.012 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-193 / Mutation: N56Q, N92Q, F176V, N187Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 4 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 110 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CL / |
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#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 12% PEG 20000, 0.1 M MES (pH 6.5), 4% Zwittergent 3-14 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→46.55 Å / Num. obs: 37895 / % possible obs: 99.7 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.902 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5925 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AY4 Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.768 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.322 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→20 Å
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