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Yorodumi- PDB-2ql1: Structural Characterization of a Mutated, ADCC-Enhanced Human Fc ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ql1 | |||||||||
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Title | Structural Characterization of a Mutated, ADCC-Enhanced Human Fc Fragment | |||||||||
Components | IGHM protein | |||||||||
Keywords | IMMUNE SYSTEM / antibody / ADCC / Fc fragment / mutation | |||||||||
Function / homology | Function and homology information complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / antigen binding / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.534 Å | |||||||||
Authors | Oganesyan, V. / Wu, H. / Dall'Acqua, W.F. | |||||||||
Citation | Journal: Mol.Immunol. / Year: 2008 Title: Structural characterization of a mutated, ADCC-enhanced human Fc fragment Authors: Oganesyan, V. / Damschroder, M.M. / Leach, W. / Wu, H. / Dall'Acqua, W.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ql1.cif.gz | 62.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ql1.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ql1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/2ql1 ftp://data.pdbj.org/pub/pdb/validation_reports/ql/2ql1 | HTTPS FTP |
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-Related structure data
Related structure data | 2dtq 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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Details | The second part of the biological assembly is generated by the two fold axis: -x, y, -z+1/2 |
-Components
#1: Protein | Mass: 25454.795 Da / Num. of mol.: 1 / Fragment: Antibody Fc fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHM / Cell line (production host): mammalian / Strain (production host): HEK 293 / References: UniProt: Q6PJF1, UniProt: P01857*PLUS | ||
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#2: 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-ZN / #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: 2.68 Å3/Da / Density % sol: 54.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 8% PEG 3350, 200 mM Zn Acetate, 5% Glycerol, 0.1 M Imidazole -Malate buffer, pH 8.0, VAPOR DIFFUSION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 1, 2007 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→47.25 Å / Num. all: 8675 / Num. obs: 8675 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.159 / Rsym value: 0.159 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.53→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1.9 / Num. unique all: 924 / Rsym value: 0.614 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DTQ 2dtq Resolution: 2.534→47.25 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.859 / SU B: 27.075 / SU ML: 0.312 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.824 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 36.253 Å2
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Refinement step | Cycle: LAST / Resolution: 2.534→47.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.534→2.6 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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