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Open data
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Basic information
Entry | Database: PDB / ID: 5hys | ||||||||||||
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Title | Structure of IgE complexed with omalizumab | ||||||||||||
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![]() | IMMUNE SYSTEM | ||||||||||||
Function / homology | ![]() adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / type 2 immune response ...adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / type 2 immune response / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / mast cell degranulation / B cell proliferation / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / complement activation, classical pathway / FCERI mediated MAPK activation / antigen binding / B cell receptor signaling pathway / FCERI mediated NF-kB activation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / inflammatory response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Pennington, L.F. / Tarchevskaya, S.S. / Sathiyamoorthy, K. / Jardetzky, T.S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of omalizumab therapy and omalizumab-mediated IgE exchange. Authors: Pennington, L.F. / Tarchevskaya, S. / Brigger, D. / Sathiyamoorthy, K. / Graham, M.T. / Nadeau, K.C. / Eggel, A. / Jardetzky, T.S. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 509.9 KB | Display | ![]() |
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PDB format | ![]() | 419.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 84.9 KB | Display | |
Data in CIF | ![]() | 115.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 8 molecules HACELBDF
#1: Antibody | Mass: 23653.387 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 23922.287 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein / Sugars , 2 types, 8 molecules GIJK
#3: Protein | Mass: 25637.812 Da / Num. of mol.: 4 / Fragment: Ig-like 3 and Ig-like 4 domains, residues 209-428 / Mutation: C328A, G335C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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-Non-polymers , 2 types, 107 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.29 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M Lithium Sulfate, 0.1 M Tris pH 8.5, and 41% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2015 / Details: Rh coated |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→37.61 Å / Num. obs: 107558 / % possible obs: 97.8 % / Observed criterion σ(F): 1.94 / Observed criterion σ(I): -3 / Redundancy: 26.9 % / Biso Wilson estimate: 61.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1148 / Rsym value: 0.1169 / Net I/σ(I): 22.09 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 23 % / Rmerge(I) obs: 2.009 / Mean I/σ(I) obs: 1.94 / % possible all: 95.73 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GT7 and 4X7S Resolution: 2.5→37.607 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 155.6 Å2 / Biso mean: 71.0647 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→37.607 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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