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Open data
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Basic information
Entry | Database: PDB / ID: 2d48 | ||||||
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Title | Crystal structure of the Interleukin-4 variant T13D | ||||||
![]() | Interleukin-4 | ||||||
![]() | CYTOKINE / four helix bundle | ||||||
Function / homology | ![]() positive regulation of eosinophil chemotaxis / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / B cell costimulation / negative regulation of complement-dependent cytotoxicity / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling ...positive regulation of eosinophil chemotaxis / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / B cell costimulation / negative regulation of complement-dependent cytotoxicity / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / negative regulation of T-helper 17 cell differentiation / dendritic cell differentiation / positive regulation of T-helper 2 cell cytokine production / positive regulation of isotype switching to IgG isotypes / neuroinflammatory response / interleukin-4-mediated signaling pathway / macrophage activation / positive regulation of interleukin-13 production / myeloid dendritic cell differentiation / positive regulation of mast cell degranulation / regulation of phosphorylation / positive regulation of mononuclear cell migration / positive regulation of amyloid-beta clearance / type 2 immune response / activation of Janus kinase activity / positive regulation of MHC class II biosynthetic process / T-helper 2 cell differentiation / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of T cell differentiation / positive regulation of myoblast fusion / positive regulation of ATP biosynthetic process / negative regulation of osteoclast differentiation / negative regulation of acute inflammatory response / positive regulation of interleukin-10 production / positive regulation of macroautophagy / negative regulation of tumor necrosis factor production / regulation of immune response / negative regulation of endothelial cell apoptotic process / positive regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of defense response to virus by host / T cell activation / cholesterol metabolic process / B cell differentiation / innate immune response in mucosa / cytokine activity / negative regulation of extrinsic apoptotic signaling pathway / microglial cell activation / growth factor activity / negative regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / positive regulation of cell migration / immune response / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kraich, M. / Klein, M. / Patino, E. / Harrer, H. / Sebald, W. / Mueller, T.D. | ||||||
![]() | ![]() Title: A modular interface of IL-4 allows for scalable affinity without affecting specificity for the IL-4 receptor Authors: Kraich, M. / Klein, M. / Patino, E. / Harrer, H. / Nickel, J. / Sebald, W. / Mueller, T.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 | ![]() | 43.5 KB | Display | ![]() |
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PDB format | ![]() | 29.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.6 KB | Display | ![]() |
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Full document | ![]() | 443.8 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b8uC ![]() 2b8xC ![]() 2b8yC ![]() 2b8zC ![]() 2b90C ![]() 2b91C ![]() 1hikS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15003.232 Da / Num. of mol.: 1 / Mutation: T13D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 52% Ammonium sulfate, 0.1M Sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 17, 2002 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9178 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→10.6 Å / Num. all: 23378 / Num. obs: 22700 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 5.2 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HIK Resolution: 1.65→9.98 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.912 / SU B: 1.777 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.067 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→9.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.692 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 15.172 Å / Origin y: 29.498 Å / Origin z: -14.073 Å
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