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Yorodumi- PDB-1t89: CRYSTAL STRUCTURE OF A HUMAN TYPE III FC GAMMA RECEPTOR IN COMPLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t89 | ||||||||||||
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Title | CRYSTAL STRUCTURE OF A HUMAN TYPE III FC GAMMA RECEPTOR IN COMPLEX WITH AN FC FRAGMENT OF IGG1 (HEXAGONAL) | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Fc gamma receptor / IgG1 / CD16 / FcgRIII / immunoglobulin | ||||||||||||
Function / homology | Function and homology information GPI anchor binding / Post-translational modification: synthesis of GPI-anchored proteins / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / IgG binding / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation ...GPI anchor binding / Post-translational modification: synthesis of GPI-anchored proteins / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / IgG binding / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / regulation of immune response / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / side of membrane / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / secretory granule membrane / antigen binding / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / transmembrane signaling receptor activity / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / cell surface receptor signaling pathway / immune response / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||||||||
Authors | Radaev, S. / Motyka, S. / Fridman, W.-H. / Sautes-Fridman, C. / Sun, P.D. | ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: The structure of a human type III Fcgamma receptor in complex with Fc Authors: Radaev, S. / Motyka, S. / Fridman, W.-H. / Sautes-Fridman, C. / Sun, P.D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t89.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t89.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 1t89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/1t89 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/1t89 | HTTPS FTP |
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-Related structure data
Related structure data | 1t83C 1fc1S 1fnlS C: citing same article (ref.) 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
#1: Antibody | Mass: 25267.645 Da / Num. of mol.: 2 / Fragment: Fc fragment of human IgG1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 9857753, UniProt: P01857*PLUS #2: Protein | | Mass: 20103.416 Da / Num. of mol.: 1 / Fragment: Fc gamma receptor type III Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75015 #3: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[beta-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 #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-alpha-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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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: 4 Å3/Da / Density % sol: 69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 Details: PEG4000, HEPES, pH 6.0, VAPOR DIFFUSION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→100 Å / Num. obs: 15541 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 82 Å2 / Rsym value: 0.087 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 3.5→3.6 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4 / Rsym value: 0.42 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FNL AND 1FC1 Resolution: 3.5→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.5→10 Å
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Refine LS restraints |
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Xplor file |
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