+Open data
-Basic information
Entry | Database: PDB / ID: 3do3 | |||||||||
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Title | Human 1gG1 Fc fragment, 2.5 Angstrom structure | |||||||||
Components | Ig gamma-1 chain C region | |||||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin fold / Glycoprotein / Immunoglobulin C region / Immunoglobulin domain / Secreted | |||||||||
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) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Braden, B.C. | |||||||||
Citation | Journal: To be Published Title: Human 1gG1 Fc fragment, 2.5 Angstrom structure. Authors: Braden, B.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3do3.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3do3.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 3do3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/3do3 ftp://data.pdbj.org/pub/pdb/validation_reports/do/3do3 | HTTPS FTP |
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-Related structure data
Related structure data | 2hwzS 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 | Chains A and B form the biological unit (Fc domain heavy chain contains domains CH3 and CH4) |
-Components
#1: Protein | Mass: 24007.137 Da / Num. of mol.: 2 Fragment: Fc domain including CH2 and CH3 regions: UNP Residues 119-330 Source method: isolated from a genetically manipulated source Details: Intact, humanized IgG1 Medi-524 produced in hybridomas. Fc fragment produced by papain digestion Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Mus musculus (house mouse) / Strain (production host): Mouse NSO cells / References: UniProt: P01857 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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: 2.93 Å3/Da / Density % sol: 58.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 20% PEG 3350, 0.2M NaCl pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 18, 2002 / Details: Confocal mirrors |
Radiation | Monochromator: Confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→17.5 Å / Num. all: 20063 / Num. obs: 19709 / % possible obs: 98 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.028 |
Reflection shell | Resolution: 2.49→2.58 Å / Rmerge(I) obs: 0.17 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2HWZ Resolution: 2.5→17.5 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.5→17.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.52 Å /
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