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- PDB-8dj7: The complex structure between human IgG1 Fc and its high affinity... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dj7 | ||||||
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Title | The complex structure between human IgG1 Fc and its high affinity receptor FcgRI H174R variant | ||||||
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![]() | IMMUNE SYSTEM / High affinity IgG1 Fc receptor | ||||||
Function / homology | ![]() high-affinity IgG receptor activity / IgG receptor activity / positive regulation of type III hypersensitivity / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / IgG binding / antibody-dependent cellular cytotoxicity ...high-affinity IgG receptor activity / IgG receptor activity / positive regulation of type III hypersensitivity / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / IgG binding / antibody-dependent cellular cytotoxicity / Cross-presentation of soluble exogenous antigens (endosomes) / Classical antibody-mediated complement activation / phagocytosis, engulfment / Initial triggering of complement / antigen processing and presentation of exogenous peptide antigen via MHC class I / positive regulation of protein tyrosine kinase activity / FCGR activation / Role of phospholipids in phagocytosis / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / receptor-mediated endocytosis / complement activation, classical pathway / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / clathrin-coated endocytic vesicle membrane / Regulation of actin dynamics for phagocytic cup formation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / early endosome membrane / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / cell surface receptor signaling pathway / blood microparticle / defense response to bacterium / immune response / external side of plasma membrane / innate immune response / signal transduction / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lu, J. / Sun, P.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Fc gamma RI FG-loop functions as a pH sensitive switch for IgG binding and release. Authors: Lu, J. / Spencer, M. / Zou, Z. / Traver, M. / Brzostowski, J. / Sun, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 300.9 KB | Display | ![]() |
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PDB format | ![]() | 241.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 38.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dinC ![]() 8dirC ![]() 4x4mS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 3 molecules BAC
#1: Protein | Mass: 24698.955 Da / Num. of mol.: 2 / Fragment: CH2 and CH3 regions, residues 112-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 31201.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules
#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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#4: 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 |
-Non-polymers , 2 types, 124 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.2M Magnesium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→50 Å / Num. obs: 37909 / % possible obs: 96.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 51.03 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.39→2.46 Å / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1953 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4x4m Resolution: 2.39→37.17 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 201.04 Å2 / Biso mean: 69.657 Å2 / Biso min: 26.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.39→37.17 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: 37.5998 Å / Origin y: -48.1481 Å / Origin z: 7.4835 Å
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Refinement TLS group |
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