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Yorodumi- PDB-1oqo: Complex between G0 version of an Fc bound to a minimized version ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oqo | ||||||||||||
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Title | Complex between G0 version of an Fc bound to a minimized version of Protein A called Mini-Z | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / Glycosylation / Oligosaccharides / IgG / Fc Fragment / Z34C / Protein A | ||||||||||||
Function / homology | Function and homology information complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | Raju, T.S. / Mulkerrin, M.G. / Parker, M. / De Vos, A.M. / Gazzano-Santoro, H. / Totpal, K. / Ultsch, M.H. | ||||||||||||
Citation | Journal: To be Published Title: Impact of Fc Glycans on The Effector Functions Vary with the Antibody mechanism of Action Authors: Raju, T.S. / Mulkerrin, M.G. / Parker, M. / De Vos, A.M. / Gazzano-Santoro, H. / Totpal, K. / Ultsch, M.H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oqo.cif.gz | 119.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oqo.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 1oqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/1oqo ftp://data.pdbj.org/pub/pdb/validation_reports/oq/1oqo | HTTPS FTP |
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-Related structure data
Related structure data | 1oqxC 1l6xS 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
#1: Antibody | Mass: 23975.072 Da / Num. of mol.: 2 / Fragment: FC FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: GenBank: 184747, UniProt: P01857*PLUS #2: Protein/peptide | Mass: 4190.682 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Phage Optimized sequence from the B-domain of Protein A Staphylococcus Aureus. Peptide Prepared using N-FMOC chemistry on Wang resin. Source: (synth.) synthetic construct (others) #3: 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-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-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-alpha-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-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 #5: 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: 2.5 Å3/Da / Density % sol: 50.35 % |
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Crystal grow | Temperature: 323 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG 550 MME, 0.1M NaOAc, 0.25M NaCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 323K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 27, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→99 Å / Num. all: 27051 / Num. obs: 27051 / % possible obs: 99.7 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 4 % / Biso Wilson estimate: 31.5 Å2 |
Reflection shell | Resolution: 2.29→2.37 Å / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1L6X Resolution: 2.3→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 42.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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