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- PDB-3wn5: Crystal structure of asymmetrically engineered Fc variant in comp... -
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Basic information
Entry | Database: PDB / ID: 3wn5 | |||||||||
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Title | Crystal structure of asymmetrically engineered Fc variant in complex with FcgRIIIa | |||||||||
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![]() | IMMUNE SYSTEM / RECEPTOR COMPLEX / FC RECEPTOR / ANTIBODY | |||||||||
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 / Fc-gamma receptor I complex binding / natural killer cell activation / complement-dependent cytotoxicity ...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 / Fc-gamma receptor I complex binding / natural killer cell activation / complement-dependent cytotoxicity / IgG immunoglobulin complex / positive regulation of natural killer cell proliferation / antibody-dependent cellular cytotoxicity / IgG binding / natural killer cell mediated cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / antigen binding / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / calcium-mediated signaling / Regulation of actin dynamics for phagocytic cup formation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / cell surface receptor signaling pathway / immune response / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kadono, S. / Mimoto, F. / Katada, H. / Igawa, T. / Kamikawa, T. / Hattori, K. | |||||||||
![]() | ![]() Title: Crystal structure of a novel asymmetrically engineered Fc variant with improved affinity for Fc gamma Rs. Authors: Mimoto, F. / Kadono, S. / Katada, H. / Igawa, T. / Kamikawa, T. / Hattori, 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 | ![]() | 255.1 KB | Display | ![]() |
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PDB format | ![]() | 208.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Ig gamma-1 chain C ... , 2 types, 4 molecules ADBE
#1: Protein | Mass: 25850.166 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 99-328 Mutation: C220S, D270E, K326D, A330K, K334E, D356C, T366S, L368A, Y407V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 26227.625 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 99-328 Mutation: C220S, L234Y, L235Y, G236W, S239M, H268D, S298A, A327D, Y349C, T366W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Protein , 1 types, 2 molecules CF
#3: Protein | Mass: 22626.307 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 18-208 / Mutation: N35Q, N71Q, N166Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 5 types, 8 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 57 molecules ![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-IOD / #10: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE CONFLICT VAL158 IS RELATED TO A NATURALLY OCCURRING VARIATION IN THE SEQUENCE OF HFCGIIIA |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.66 % |
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Crystal grow | Temperature: 293 K / pH: 6.25 Details: 14.5% PEG 3350, 0.1M Bis-Tris, 0.2M Sodium Iodide, Streak seeding, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2012 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→49.03 Å / Num. obs: 43675 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 51.96 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.91 |
Reflection shell | Resolution: 2.78→2.85 Å / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.09 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.78→25 Å
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