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- PDB-1ijz: Solution Structure of Human IL-13 -

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Basic information

Entry
Database: PDB / ID: 1ijz
TitleSolution Structure of Human IL-13
ComponentsINTERLEUKIN-13
KeywordsCYTOKINE / left-handed four-helix bundle
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 / positive regulation of immunoglobulin production / cellular response to cytokine stimulus / positive regulation of interleukin-10 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 / cytokine activity / positive regulation of protein secretion / positive regulation of smooth muscle cell proliferation / microglial cell activation / response to nicotine / negative regulation of inflammatory response / cellular response to mechanical stimulus / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / response to ethanol / response to lipopolysaccharide / inflammatory response / immune response / external side of plasma membrane / positive regulation of gene expression / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Interleukin-13 / Interleukin-13 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMoy, F.J. / Diblasio, E. / Wilhelm, J. / Powers, R.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Solution structure of human IL-13 and implication for receptor binding.
Authors: Moy, F.J. / Diblasio, E. / Wilhelm, J. / Powers, R.
History
DepositionMay 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERLEUKIN-13


Theoretical massNumber of molelcules
Total (without water)12,4911
Polymers12,4911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein INTERLEUKIN-13 / IL-13


Mass: 12490.583 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35225

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
3233D 13C-separated NOESY
232HNCA-J
242HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM interleukin-13 U-15N; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl 90% H2O, 10% D2O; pH 6.090% H2O/10% D2O
21mM interleukin-13 U-15N,U-13C; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl 90% H2O, 10% D2O; pH 6.090% H2O/10% D2O
31mM interleukin-13 U-15N,U-13C; 40mM phosphate buffer; 2mM NaN3; 40 mM NaCl; 100% D2O; pH 6.0100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
140 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl 6.0 ambient 298 K
240 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl 6.0 ambient 298 K
340 mM sodium phosphate, 2 mM NaN3, 40 mM NaCl 6.0 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2Brukercollection
NMRPipe97.231.15.18Delaglioprocessing
X-PLOR3.84Brumgerrefinement
PIPP4.2.8Garrettdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2848 restraints, 2248 are NOE-derived distance constraints, 299 dihedral angle restraints,50 distance restraints from hydrogen bonds, 205 Ca/Cb ...Details: The structures are based on a total of 2848 restraints, 2248 are NOE-derived distance constraints, 299 dihedral angle restraints,50 distance restraints from hydrogen bonds, 205 Ca/Cb constraints, 96 coupling constant constraints. Additionally, a ramachandran conformational database and radius of gyration target function was used during the refinement.
NMR ensembleConformers submitted total number: 1

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