+Open data
-Basic information
Entry | Database: PDB / ID: 5e4e | ||||||
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Title | Engineered Interleukin-13 bound to receptor | ||||||
Components |
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Keywords | SIGNALING PROTEIN / agonist-receptor complex / protein engineering | ||||||
Function / homology | Function and homology information interleukin-13 receptor complex / interleukin-4 receptor activity / interleukin-13 receptor binding / negative regulation of lung ciliated cell differentiation / positive regulation of lung goblet cell differentiation / positive regulation of pancreatic stellate cell proliferation / regulation of proton transport / positive regulation of connective tissue growth factor production / production of molecular mediator involved in inflammatory response / negative regulation of T-helper 1 cell differentiation ...interleukin-13 receptor complex / interleukin-4 receptor activity / interleukin-13 receptor binding / negative regulation of lung ciliated cell differentiation / positive regulation of lung goblet cell differentiation / positive regulation of pancreatic stellate cell proliferation / regulation of proton transport / positive regulation of connective tissue growth factor production / production of molecular mediator involved in inflammatory response / negative regulation of T-helper 1 cell differentiation / negative regulation of complement-dependent cytotoxicity / T-helper 1 cell differentiation / Interleukin-18 signaling / positive regulation of T-helper 2 cell differentiation / negative regulation of transforming growth factor beta production / interleukin-4-mediated signaling pathway / macrophage activation / positive regulation of mast cell degranulation / positive regulation of macrophage activation / T-helper 2 cell differentiation / cytokine receptor activity / positive regulation of myoblast fusion / cytokine binding / defense response to protozoan / cellular response to cytokine stimulus / positive regulation of interleukin-10 production / immunoglobulin mediated immune response / positive regulation of immunoglobulin production / centriolar satellite / negative regulation of endothelial cell apoptotic process / positive regulation of B cell proliferation / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of release of sequestered calcium ion into cytosol / response to nicotine / cytokine activity / positive regulation of protein secretion / microglial cell activation / positive regulation of smooth muscle cell proliferation / negative regulation of inflammatory response / cytokine-mediated signaling pathway / cellular response to mechanical stimulus / positive regulation of cold-induced thermogenesis / response to ethanol / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / cell surface receptor signaling pathway / receptor complex / immune response / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Moraga, I. / Thomas, C. / Jude, K.M. / Garcia, K.C. | ||||||
Citation | Journal: Sci.Signal. / Year: 2015 Title: Instructive roles for cytokine-receptor binding parameters in determining signaling and functional potency. Authors: Moraga, I. / Richter, D. / Wilmes, S. / Winkelmann, H. / Jude, K. / Thomas, C. / Suhoski, M.M. / Engleman, E.G. / Piehler, J. / Garcia, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e4e.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e4e.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 5e4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/5e4e ftp://data.pdbj.org/pub/pdb/validation_reports/e4/5e4e | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12463.391 Da / Num. of mol.: 1 / Fragment: UNP residues 34-146 / Mutation: L10V, V18I, L39R, D87S, T88S, L101F, K104R, K105T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL13, NC30 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35225 | ||
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#2: Protein | Mass: 23212.086 Da / Num. of mol.: 1 / Fragment: UNP residues 26-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL4R, IL4RA, 582J2.1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P24394 | ||
#3: Protein | Mass: 36570.961 Da / Num. of mol.: 1 / Fragment: UNP residues 23-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL13RA1, IL13R, IL13RA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P78552 | ||
#4: Chemical | ChemComp-SO4 / #5: Sugar | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.2 Details: lithium sulfate, phosphate/citrate pH 4.2, PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→38.74 Å / Num. obs: 16583 / % possible obs: 99.2 % / Redundancy: 4.2 % / Net I/σ(I): 15.6 |
-Processing
Software |
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Refinement | Resolution: 3→38.74 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 31.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→38.74 Å
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Refine LS restraints |
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LS refinement shell |
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