+Open data
-Basic information
Entry | Database: PDB / ID: 5d6d | |||||||||
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Title | Crystal structure of GASDALIE IgG1 Fc in complex with FcgRIIIa | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / ADCC / IgG | |||||||||
Function / homology | Function and homology information 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 / Fc-gamma receptor I complex binding / natural killer cell activation ...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 / 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 / Classical antibody-mediated complement activation / Initial triggering of complement / 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 / Regulation of Complement cascade / calcium-mediated signaling / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / 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 / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / cell surface receptor signaling pathway / blood microparticle / 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: 3.13 Å | |||||||||
Authors | Ahmed, A.A. / Bjorkman, P.J. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2016 Title: Structural characterization of GASDALIE Fc bound to the activating Fc receptor Fc gamma RIIIa. Authors: Ahmed, A.A. / Keremane, S.R. / Vielmetter, J. / Bjorkman, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d6d.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d6d.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 5d6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d6d_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5d6d_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5d6d_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 5d6d_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/5d6d ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d6d | HTTPS FTP |
-Related structure data
Related structure data | 5d4qC 3sgkS S: Starting model for refinement C: citing same article (ref.) |
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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: 28105.951 Da / Num. of mol.: 2 / Fragment: UNP residues 109-329 / Mutation: G236A, S239D,A330L, I332E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Homo sapiens (human) / References: UniProt: P01857 #2: Protein | | Mass: 27086.391 Da / Num. of mol.: 1 / Fragment: UNP residues 14-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR3A, CD16A, FCG3, FCGR3, IGFR3 / Production host: Homo sapiens (human) / References: UniProt: P08637 |
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-Sugars , 4 types, 5 molecules
#3: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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 |
#5: Sugar | ChemComp-FUC / |
#6: Sugar |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: grown in sitting drop vapor diffusion by mixing equal volumes of protein (10 mg/ml) with a solution containing 0.04 M potassium dihydrogen phosphate and 16% (w/v) PEG 8000 at 293.15 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.13→71.31 Å / Num. obs: 14045 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.52 |
Reflection shell | Resolution: 3.13→3.18 Å / Mean I/σ(I) obs: 0.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SGK Resolution: 3.13→71.309 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.13→71.309 Å
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Refine LS restraints |
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LS refinement shell |
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