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Yorodumi- PDB-3ay4: Crystal structure of nonfucosylated Fc complexed with bis-glycosy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ay4 | |||||||||
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Title | Crystal structure of nonfucosylated Fc complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / COMPLEX / FC FRAGMENT / IGG / RECEPTOR / CD16 / GAMMA | |||||||||
Function / homology | Function and homology information immune receptor activity / low-affinity IgG receptor activity / natural killer cell degranulation / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / macrophage activation / natural killer cell mediated cytotoxicity / natural killer cell activation / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity ...immune receptor activity / low-affinity IgG receptor activity / natural killer cell degranulation / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / macrophage activation / natural killer cell mediated cytotoxicity / natural killer cell activation / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / IgG binding / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / positive regulation of natural killer cell proliferation / FCGR activation / regulation of immune response / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of Complement cascade / calcium-mediated signaling / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / positive regulation of tumor necrosis factor production / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Mizushima, T. / Takemoto, E. / Yagi, H. / Shibata-Koyama, M. / Isoda, Y. / Iida, S. / Satoh, M. / Kato, K. | |||||||||
Citation | Journal: Genes Cells / Year: 2011 Title: Structural basis for improved efficacy of therapeutic antibodies on defucosylation of their Fc glycans Authors: Mizushima, T. / Yagi, H. / Takemoto, E. / Shibata-Koyama, M. / Isoda, Y. / Iida, S. / Masuda, K. / Satoh, M. / Kato, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ay4.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ay4.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ay4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/3ay4 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/3ay4 | HTTPS FTP |
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-Related structure data
Related structure data | 1e4kS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 25097.434 Da / Num. of mol.: 2 / Fragment: Fc fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Plasmid: PKANTEX2160 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): MS704 / References: UniProt: P01857 #2: Protein | | Mass: 20641.012 Da / Num. of mol.: 1 / Fragment: Extracellular domain / Mutation: N38Q,N74Q,N169Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR3A / Plasmid: pKANTEX93 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08637 |
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-Sugars , 3 types, 4 molecules
#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)-[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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 |
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-Non-polymers , 1 types, 307 molecules
#6: Water | ChemComp-HOH / |
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-Details
Sequence details | THIS SEQUENCE IS CAUSED BY NATURAL VARIANT (REF 11 OF UNP DATABASE, P08637) |
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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: 3.69 Å3/Da / Density % sol: 66.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 12% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 7, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→87.6 Å / Num. obs: 53300 / % possible obs: 96.4 % / Observed criterion σ(F): -3 / Redundancy: 12.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.372 / % possible all: 77.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1E4K Resolution: 2.2→43.79 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / ESU R Free: 0.195 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.491 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→43.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.202→2.259 Å / Total num. of bins used: 20
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