+Open data
-Basic information
Entry | Database: PDB / ID: 2b8y | ||||||
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Title | Crystal structure of the interleukin-4 variant T13DF82D | ||||||
Components | Interleukin-4 | ||||||
Keywords | CYTOKINE / Four Helix Bundle | ||||||
Function / homology | Function and homology information interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / negative regulation of complement-dependent cytotoxicity / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / positive regulation of T-helper 2 cell cytokine production / dendritic cell differentiation ...interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / negative regulation of complement-dependent cytotoxicity / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / positive regulation of T-helper 2 cell cytokine production / dendritic cell differentiation / neuroinflammatory response / interleukin-4-mediated signaling pathway / positive regulation of isotype switching to IgG isotypes / macrophage activation / positive regulation of interleukin-13 production / myeloid dendritic cell differentiation / positive regulation of amyloid-beta clearance / activation of Janus kinase activity / type 2 immune response / regulation of phosphorylation / positive regulation of MHC class II biosynthetic process / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of T cell differentiation / positive regulation of ATP biosynthetic process / negative regulation of osteoclast differentiation / positive regulation of macroautophagy / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / regulation of immune response / negative regulation of endothelial cell apoptotic process / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of B cell proliferation / positive regulation of T cell proliferation / cholesterol metabolic process / B cell differentiation / T cell activation / cytokine activity / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kraich, M. / Klein, M. / Patino, E. / Harrer, H. / Sebald, W. / Mueller, T.D. | ||||||
Citation | Journal: Bmc Biol. / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b8y.cif.gz | 43.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b8y.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 2b8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b8y_validation.pdf.gz | 438.1 KB | Display | wwPDB validaton report |
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Full document | 2b8y_full_validation.pdf.gz | 440.1 KB | Display | |
Data in XML | 2b8y_validation.xml.gz | 9 KB | Display | |
Data in CIF | 2b8y_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/2b8y ftp://data.pdbj.org/pub/pdb/validation_reports/b8/2b8y | HTTPS FTP |
-Related structure data
Related structure data | 2b8uC 2b8xC 2b8zC 2b90C 2b91C 2d48C 1hikS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14971.145 Da / Num. of mol.: 1 / Mutation: T13D, F82D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P05112 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 61.37 % |
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Crystal grow | Temperature: 294 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 294K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2003 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20.5 Å / Num. all: 18425 / Num. obs: 18359 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HIK Resolution: 1.8→14.79 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.983 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.116 / 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: 26.363 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→14.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 15.072 Å / Origin y: 29.535 Å / Origin z: -14.12 Å
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