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Yorodumi- PDB-3ry4: 1.5 Angstrom resolution structure of glycosylated fcgammariia (lo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ry4 | ||||||
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Title | 1.5 Angstrom resolution structure of glycosylated fcgammariia (low-responder polymorphism) | ||||||
Components | Low affinity immunoglobulin gamma Fc region receptor II-a | ||||||
Keywords | IMMUNE SYSTEM / FC RECEPTOR / CD32 / IMMUNOGLOBULIN SUPERFAMILY / LOW RESPONDER POLYMORPHISM / CELL MEMBRANE / GLYCOPROTEIN / IGG-BINDING PROTEIN / IMMUNOGLOBULIN DOMAIN / MEMBRANE / PHOSPHOPROTEIN / RECEPTOR / TRANSMEMBRANE | ||||||
Function / homology | Function and homology information IgG receptor activity / antibody-dependent cellular cytotoxicity / IgG binding / FCGR activation / Role of phospholipids in phagocytosis / positive regulation of phagocytosis / FCGR3A-mediated IL10 synthesis / secretory granule membrane / Regulation of actin dynamics for phagocytic cup formation / positive regulation of tumor necrosis factor production ...IgG receptor activity / antibody-dependent cellular cytotoxicity / IgG binding / FCGR activation / Role of phospholipids in phagocytosis / positive regulation of phagocytosis / FCGR3A-mediated IL10 synthesis / secretory granule membrane / Regulation of actin dynamics for phagocytic cup formation / positive regulation of tumor necrosis factor production / cell surface receptor signaling pathway / external side of plasma membrane / Neutrophil degranulation / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Ramsland, P.A. / Farrugia, W. / Hogarth, P.M. | ||||||
Citation | Journal: J.Immunol. / Year: 2011 Title: Structural Basis for Fc{gamma}RIIa Recognition of Human IgG and Formation of Inflammatory Signaling Complexes. Authors: Ramsland, P.A. / Farrugia, W. / Bradford, T.M. / Sardjono, C.T. / Esparon, S. / Trist, H.M. / Powell, M.S. / Tan, P.S. / Cendron, A.C. / Wines, B.D. / Scott, A.M. / Hogarth, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ry4.cif.gz | 55.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ry4.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ry4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ry4_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 3ry4_full_validation.pdf.gz | 461.5 KB | Display | |
Data in XML | 3ry4_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 3ry4_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/3ry4 ftp://data.pdbj.org/pub/pdb/validation_reports/ry/3ry4 | HTTPS FTP |
-Related structure data
Related structure data | 3ry5C 3ry6C 1fcgS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19187.449 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, residues 37-206 / Mutation: S88P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: CD32, FCG2, FCGR2A, FCGR2A1, IGFR2 / Plasmid: PVL1392 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12318 |
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#2: Sugar | ChemComp-NAG / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.55 % |
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Crystal grow | Method: vapor diffusion / pH: 5.6 Details: 30% (W/V) PEG 4000, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, PH 5.60, VAPOR DIFFUSION, TEMPERATURE 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2002 / Details: BENT CONICAL SI-MIRROR (RH COATED) |
Radiation | Monochromator: BENT GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 35275 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 20.3 Å2 / Rsym value: 0.052 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.32 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FCG Resolution: 1.5→19.84 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.55 Å / Rfactor Rfree error: 0.031 /
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