+Open data
-Basic information
Entry | Database: PDB / ID: 4ps4 | ||||||||||||
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Title | Crystal structure of the complex between IL-13 and M1295 FAB | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / ALPHA-HELICAL BUNDLE / CYTOKINE / DISULFIDE BOND / GLYCOPROTEIN / SECRETED / MONOCLONAL ANTIBODY | ||||||||||||
Function / homology | Function and homology information 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 / negative regulation of complement-dependent cytotoxicity / Interleukin-18 signaling / negative regulation of transforming growth factor beta production / macrophage activation ...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 / negative regulation of complement-dependent cytotoxicity / Interleukin-18 signaling / negative regulation of transforming growth factor beta production / macrophage activation / positive regulation of mast cell degranulation / positive regulation of macrophage activation / cellular response to cytokine stimulus / positive regulation of interleukin-10 production / positive regulation of immunoglobulin production / negative regulation of endothelial cell apoptotic process / positive regulation of B cell proliferation / 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 / cellular response to mechanical stimulus / positive regulation of cold-induced thermogenesis / response to ethanol / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / immune response / inflammatory response / external side of plasma membrane / positive regulation of gene expression / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.8 Å | ||||||||||||
Authors | Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Human Framework Adaptation of a Mouse Anti-Human Il-13 Antibody. Authors: Fransson, J. / Teplyakov, A. / Raghunathan, G. / Chi, E. / Cordier, W. / Dinh, T. / Feng, Y. / Giles-Komar, J. / Gilliland, G. / Lollo, B. / Malia, T.J. / Nishioka, W. / Obmolova, G. / Zhao, ...Authors: Fransson, J. / Teplyakov, A. / Raghunathan, G. / Chi, E. / Cordier, W. / Dinh, T. / Feng, Y. / Giles-Komar, J. / Gilliland, G. / Lollo, B. / Malia, T.J. / Nishioka, W. / Obmolova, G. / Zhao, S. / Zhao, Y. / Swanson, R.V. / Almagro, J.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ps4.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ps4.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ps4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/4ps4 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/4ps4 | HTTPS FTP |
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-Related structure data
Related structure data | 3l5wC 3l5xSC 3l7fC 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
#1: Antibody | Mass: 23358.986 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo Sapiens (human) |
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#2: Antibody | Mass: 24543.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo Sapiens (human) |
#3: Protein | Mass: 12490.583 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 35-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL13, NC30 / Production host: Escherichia coli (E. coli) / References: UniProt: P35225 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M SODIUM ACETATE PH 4.5, 25% PEG 8K, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 7, 2008 / Details: VARIMAX HF |
Radiation | Monochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 12722 / Num. obs: 12722 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.8 / % possible all: 62.5 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 3L5X Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.852 / SU B: 18.934 / SU ML: 0.357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.45 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.817→2.888 Å / Total num. of bins used: 20
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