+Open data
-Basic information
Entry | Database: PDB / ID: 7shy | ||||||
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Title | IgE-Fc in complex with omalizumab scFv | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IgE / omalizumab / xolair / inhibitor | ||||||
Function / homology | Function and homology information 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 / antigen binding / FCERI mediated MAPK activation / B cell receptor signaling pathway / FCERI mediated NF-kB activation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / inflammatory response / immune response / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Pennington, L.F. / Jardetzky, T.J. / Kleinboelting, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Directed evolution of and structural insights into antibody-mediated disruption of a stable receptor-ligand complex. Authors: Luke F Pennington / Pascal Gasser / Silke Kleinboelting / Chensong Zhang / Georgios Skiniotis / Alexander Eggel / Theodore S Jardetzky / Abstract: Antibody drugs exert therapeutic effects via a range of mechanisms, including competitive inhibition, allosteric modulation, and immune effector mechanisms. Facilitated dissociation is an additional ...Antibody drugs exert therapeutic effects via a range of mechanisms, including competitive inhibition, allosteric modulation, and immune effector mechanisms. Facilitated dissociation is an additional mechanism where antibody-mediated "disruption" of stable high-affinity macromolecular complexes can potentially enhance therapeutic efficacy. However, this mechanism is not well understood or utilized therapeutically. Here, we investigate and engineer the weak disruptive activity of an existing therapeutic antibody, omalizumab, which targets IgE antibodies to block the allergic response. We develop a yeast display approach to select for and engineer antibody disruptive efficiency and generate potent omalizumab variants that dissociate receptor-bound IgE. We determine a low resolution cryo-EM structure of a transient disruption intermediate containing the IgE-Fc, its partially dissociated receptor and an antibody inhibitor. Our results provide a conceptual framework for engineering disruptive inhibitors for other targets, insights into the failure in clinical trials of the previous high affinity omalizumab HAE variant and anti-IgE antibodies that safely and rapidly disarm allergic effector cells. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7shy.cif.gz | 723.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7shy.ent.gz | 603.2 KB | Display | PDB format |
PDBx/mmJSON format | 7shy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7shy_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7shy_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7shy_validation.xml.gz | 69.5 KB | Display | |
Data in CIF | 7shy_validation.cif.gz | 94 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/7shy ftp://data.pdbj.org/pub/pdb/validation_reports/sh/7shy | HTTPS FTP |
-Related structure data
Related structure data | 7shtC 7shuC 7shzC 7si0C 5hysS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules AGHB
#3: Protein | Mass: 27550.873 Da / Num. of mol.: 4 / Fragment: C3-4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Production host: Homo sapiens (human) / References: UniProt: P01854 |
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-Antibody , 2 types, 8 molecules IKCEJLDF
#1: Antibody | Mass: 13362.744 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 14665.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Sugars , 6 types, 8 molecules
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(2-3)-[alpha-L-fucopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(2-3)-[alpha-L-fucopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source | ||
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#5: Polysaccharide | beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 | ||
#6: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 | ||
#7: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 | ||
#9: Sugar | #10: Sugar | ChemComp-MAN / | |
-Non-polymers , 2 types, 7 molecules
#8: Chemical | ChemComp-GOL / |
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#11: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 2.7 Å3/Da / Density % sol: 54.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.02 M Magnesium chloride, 0.1M HEPES pH 7.5, 22% (w/v) Polyacrylic acid 5100 sodium salt |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3→39.93 Å / Num. obs: 160286 / % possible obs: 98 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 11.78 |
Reflection shell | Resolution: 3→3.107 Å / Mean I/σ(I) obs: 1.29 / Num. unique obs: 16540 / CC1/2: 0.635 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5hys Resolution: 3→39.93 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 266.83 Å2 / Biso mean: 99.1952 Å2 / Biso min: 39 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→39.93 Å
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