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Yorodumi- PDB-8epa: Structure of interleukin receptor common gamma chain (IL2Rgamma) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8epa | ||||||
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Title | Structure of interleukin receptor common gamma chain (IL2Rgamma) in complex with two antibodies | ||||||
Components |
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Keywords | IMMUNE SYSTEM / interleukin signaling / lymphocyte maturation / blocking antibody / immunoglobulin | ||||||
Function / homology | Function and homology information interleukin-7-mediated signaling pathway / mature B cell differentiation / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / positive regulation of T cell differentiation in thymus / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway ...interleukin-7-mediated signaling pathway / mature B cell differentiation / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / positive regulation of T cell differentiation in thymus / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-2-mediated signaling pathway / STAT3 nuclear events downstream of ALK signaling / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / cytokine receptor activity / Interleukin-2 signaling / positive regulation of B cell differentiation / cytokine binding / Interleukin receptor SHC signaling / coreceptor activity / positive regulation of phagocytosis / Interleukin-7 signaling / cytokine-mediated signaling pathway / T cell differentiation in thymus / gene expression / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / receptor complex / endosome / immune response / external side of plasma membrane / positive regulation of gene expression / cell surface / endoplasmic reticulum / signal transduction / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Franklin, M.C. / Romero Hernandez, A. | ||||||
Funding support | 1items
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Citation | Journal: Sci Transl Med / Year: 2023 Title: Blocking common γ chain cytokine signaling ameliorates T cell-mediated pathogenesis in disease models. Authors: Audrey Le Floc'h / Kirsten Nagashima / Dylan Birchard / George Scott / Li-Hong Ben / Dharani Ajithdoss / Kaitlyn Gayvert / Annabel Romero Hernandez / Olivier Herbin / Amanda Tay / Pamela ...Authors: Audrey Le Floc'h / Kirsten Nagashima / Dylan Birchard / George Scott / Li-Hong Ben / Dharani Ajithdoss / Kaitlyn Gayvert / Annabel Romero Hernandez / Olivier Herbin / Amanda Tay / Pamela Farrales / Chandrashekhar K Korgaonkar / Hao Pan / Sweta Shah / Vishal Kamat / Ishita Chatterjee / Jon Popke / Adelekan Oyejide / Wei Keat Lim / Jee H Kim / Tammy Huang / Matthew Franklin / William Olson / Thomas Norton / Lorah Perlee / George D Yancopoulos / Andrew J Murphy / Matthew A Sleeman / Jamie M Orengo / Abstract: The common γ chain (γc; IL-2RG) is a subunit of the interleukin (IL) receptors for the γc cytokines IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21. The lack of appropriate neutralizing antibodies ...The common γ chain (γc; IL-2RG) is a subunit of the interleukin (IL) receptors for the γc cytokines IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21. The lack of appropriate neutralizing antibodies recognizing IL-2RG has made it difficult to thoroughly interrogate the role of γc cytokines in inflammatory and autoimmune disease settings. Here, we generated a γc cytokine receptor antibody, REGN7257, to determine whether γc cytokines might be targeted for T cell-mediated disease prevention and treatment. Biochemical, structural, and in vitro analysis showed that REGN7257 binds with high affinity to IL-2RG and potently blocks signaling of all γc cytokines. In nonhuman primates, REGN7257 efficiently suppressed T cells without affecting granulocytes, platelets, or red blood cells. Using REGN7257, we showed that γc cytokines drive T cell-mediated disease in mouse models of graft-versus-host disease (GVHD) and multiple sclerosis by affecting multiple aspects of the pathogenic response. We found that our xenogeneic GVHD mouse model recapitulates hallmarks of acute and chronic GVHD, with T cell expansion/infiltration into tissues and liver fibrosis, as well as hallmarks of immune aplastic anemia, with bone marrow aplasia and peripheral cytopenia. Our findings indicate that γc cytokines contribute to GVHD and aplastic anemia pathology by promoting these characteristic features. By demonstrating that broad inhibition of γc cytokine signaling with REGN7257 protects from immune-mediated disorders, our data provide evidence of γc cytokines as key drivers of pathogenic T cell responses, offering a potential strategy for the management of T cell-mediated diseases. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8epa.cif.gz | 133.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8epa.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 8epa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/8epa ftp://data.pdbj.org/pub/pdb/validation_reports/ep/8epa | HTTPS FTP |
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-Related structure data
Related structure data | 28523MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Antibody , 4 types, 4 molecules HLAB
#2: Antibody | Mass: 23607.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) |
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#3: Antibody | Mass: 23541.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) |
#4: Antibody | Mass: 23323.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) |
#5: Antibody | Mass: 23247.803 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) |
-Protein / Sugars , 2 types, 2 molecules I
#1: Protein | Mass: 31617.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RG / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P31785 |
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#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of IL2Rgamma extracellular domain with Fab fragments of antibodies REGN7257 and REGN9432 Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Cricetulus griseus (Chinese hamster) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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EM software | Name: EPU / Category: image acquisition | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 435563 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 114.63 Å2 | ||||||||||||||||||||||||
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