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Yorodumi- PDB-3wjj: Crystal structure of IIb selective Fc variant, Fc(P238D), in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wjj | |||||||||
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Title | Crystal structure of IIb selective Fc variant, Fc(P238D), in complex with FcgRIIb | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / RECEPTOR COMPLEX / FC RECEPTOR / ANTIBODY | |||||||||
Function / homology | Function and homology information negative regulation of type I hypersensitivity / negative regulation of antibody-dependent cellular cytotoxicity / immune effector process / follicular dendritic cell activation / immune complex clearance by monocytes and macrophages / regulation of B cell antigen processing and presentation / regulation of immune complex clearance by monocytes and macrophages / negative regulation of acute inflammatory response to antigenic stimulus / positive regulation of humoral immune response / negative regulation of neutrophil activation ...negative regulation of type I hypersensitivity / negative regulation of antibody-dependent cellular cytotoxicity / immune effector process / follicular dendritic cell activation / immune complex clearance by monocytes and macrophages / regulation of B cell antigen processing and presentation / regulation of immune complex clearance by monocytes and macrophages / negative regulation of acute inflammatory response to antigenic stimulus / positive regulation of humoral immune response / negative regulation of neutrophil activation / regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of response to endoplasmic reticulum stress / negative regulation of dendritic cell antigen processing and presentation / negative regulation of B cell receptor signaling pathway / negative regulation of humoral immune response mediated by circulating immunoglobulin / low-affinity IgG receptor activity / follicular B cell differentiation / negative regulation of cytotoxic T cell degranulation / IgG receptor activity / negative regulation of immunoglobulin production / cellular response to molecule of bacterial origin / negative regulation of dendritic cell differentiation / negative regulation of B cell activation / regulation of dendritic spine maintenance / regulation of adaptive immune response / mature B cell differentiation involved in immune response / negative regulation of macrophage activation / Fc-gamma receptor signaling pathway / negative regulation of immune response / complement-dependent cytotoxicity / regulation of signaling receptor activity / negative regulation of phagocytosis / antibody-dependent cellular cytotoxicity / IgG binding / Fc-gamma receptor I complex binding / negative regulation of cytokine production / Classical antibody-mediated complement activation / phagocytosis, engulfment / IgG immunoglobulin complex / Initial triggering of complement / negative regulation of interleukin-10 production / regulation of innate immune response / negative regulation of B cell proliferation / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / phagocytosis / positive regulation of phagocytosis / receptor-mediated endocytosis / cerebellum development / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / antigen binding / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / B cell receptor signaling pathway / response to bacterium / Regulation of actin dynamics for phagocytic cup formation / defense response / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / amyloid-beta binding / cell body / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / dendritic spine / blood microparticle / cell surface receptor signaling pathway / inflammatory response / external side of plasma membrane / protein-containing complex binding / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Kadono, S. / Mimoto, F. / Katada, H. / Igawa, T. / Kuramochi, T. / Muraoka, M. / Wada, Y. / Haraya, K. / Miyazaki, T. / Hattori, K. | |||||||||
Citation | Journal: Protein Eng.Des.Sel. / Year: 2013 Title: Engineered antibody Fc variant with selectively enhanced Fc gamma RIIb binding over both Fc gamma RIIaR131 and Fc gamma RIIaH131. Authors: Mimoto, F. / Katada, H. / Kadono, S. / Igawa, T. / Kuramochi, T. / Muraoka, M. / Wada, Y. / Haraya, K. / Miyazaki, T. / Hattori, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wjj.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wjj.ent.gz | 104.2 KB | Display | PDB format |
PDBx/mmJSON format | 3wjj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/3wjj ftp://data.pdbj.org/pub/pdb/validation_reports/wj/3wjj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25942.264 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 99-328 / Mutation: P238D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P01857 #2: Protein | | Mass: 20257.516 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 45-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD32, FCG2, FCGR2B, FCGR2C, IGFR2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P31994 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | |
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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: 2.91 Å3/Da / Density % sol: 57.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 17% PEG 3350, 0.1M Bis-Tris, 0.2M ammonium acetate, 2.7% D-galactose, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 30, 2011 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→41.5 Å / Num. all: 25593 / Num. obs: 25455 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 53.69 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1840 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.883 / WRfactor Rfree: 0.2579 / WRfactor Rwork: 0.2157 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8049 / SU B: 10.617 / SU ML: 0.234 / SU R Cruickshank DPI: 0.6047 / SU Rfree: 0.3217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.605 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
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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 max: 127.36 Å2 / Biso mean: 63.4889 Å2 / Biso min: 16.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.603→2.67 Å / Total num. of bins used: 20
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