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- PDB-2l3y: Solution structure of mouse IL-6 -

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Basic information

Entry
Database: PDB / ID: 2l3y
TitleSolution structure of mouse IL-6
ComponentsInterleukin-6
KeywordsTRANSCRIPTION / CYTOKINE / INTERLEUKIN / SIGNALING / GP-130
Function / homology
Function and homology information


positive regulation of gliogenesis / lymphocyte costimulation / negative regulation of chemokine production => GO:0032682 / negative regulation of muscle organ development / interleukin-21 production / negative regulation of cytokine production => GO:0001818 / negative regulation of membrane potential / positive regulation of immunoglobulin production => GO:0002639 / positive regulation of tumor necrosis factor production => GO:0032760 / positive regulation of tumor necrosis factor production => GO:0032760 ...positive regulation of gliogenesis / lymphocyte costimulation / negative regulation of chemokine production => GO:0032682 / negative regulation of muscle organ development / interleukin-21 production / negative regulation of cytokine production => GO:0001818 / negative regulation of membrane potential / positive regulation of immunoglobulin production => GO:0002639 / positive regulation of tumor necrosis factor production => GO:0032760 / positive regulation of tumor necrosis factor production => GO:0032760 / immunoglobulin production / glucagon secretion / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / positive regulation of miRNA processing / regulation of glucagon secretion / negative regulation of interleukin-1-mediated signaling pathway / Interleukin-6 signaling / : / hepatic immune response / regulation of vascular endothelial growth factor production / positive regulation of transmission of nerve impulse / negative regulation of primary miRNA processing / T follicular helper cell differentiation / germinal center B cell differentiation / interleukin-6 receptor complex / positive regulation of cell proliferation in bone marrow / positive regulation of extracellular matrix disassembly / positive regulation of receptor signaling pathway via STAT / positive regulation of apoptotic DNA fragmentation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / negative regulation of hormone secretion / cellular response to prolactin / hepatocyte proliferation / : / neutrophil apoptotic process / interleukin-6 receptor binding / negative regulation of collagen biosynthetic process / positive regulation of T-helper 2 cell differentiation / response to xenobiotic stimulus => GO:0009410 / regulation of circadian sleep/wake cycle, non-REM sleep / T-helper 17 cell lineage commitment / response to yeast / positive regulation of T-helper 2 cell cytokine production / response to auditory stimulus / epithelial cell proliferation involved in salivary gland morphogenesis / positive regulation of B cell activation / endocrine pancreas development / positive regulation of acute inflammatory response / vascular endothelial growth factor production / branching involved in salivary gland morphogenesis / bone remodeling / positive regulation of cytokine production involved in inflammatory response / negative regulation of bone resorption / response to caffeine / positive regulation of leukocyte adhesion to vascular endothelial cell / myeloid cell homeostasis / cellular response to hepatocyte growth factor stimulus / muscle cell cellular homeostasis / interleukin-6-mediated signaling pathway / positive regulation of interleukin-17 production / defense response to protozoan / cellular response to nutrient levels / regulation of insulin secretion / positive regulation of interleukin-10 production / positive regulation of vascular endothelial growth factor production / response to amino acid / cellular response to interleukin-1 / positive regulation of osteoblast differentiation / negative regulation of gluconeogenesis / positive regulation of epithelial to mesenchymal transition / response to electrical stimulus / positive regulation of T cell proliferation / positive regulation of chemokine production / response to glucocorticoid / positive regulation of glial cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / T cell activation / positive regulation of neuron differentiation / response to cold / cellular response to dexamethasone stimulus / cell redox homeostasis / positive regulation of DNA replication / response to activity / positive regulation of interleukin-1 beta production / cytokine activity / acute-phase response / positive regulation of translation / cellular response to estradiol stimulus / positive regulation of interleukin-8 production / positive regulation of epithelial cell proliferation / liver regeneration / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / negative regulation of protein kinase activity / growth factor activity / wound healing / response to insulin / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
Similarity search - Function
Interleukin-6 / Interleukin-6/G-CSF/MGF family / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsVeverka, V. / Redpath, N.T. / Carrington, B. / Muskett, F.W. / Taylor, R.J. / Henry, A.J. / Carr, M.D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Conservation of functional sites on interleukin-6 and implications for evolution of signaling complex assembly and therapeutic intervention.
Authors: Veverka, V. / Baker, T. / Redpath, N.T. / Carrington, B. / Muskett, F.W. / Taylor, R.J. / Lawson, A.D. / Henry, A.J. / Carr, M.D.
History
DepositionSep 25, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Jan 2, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-6


Theoretical massNumber of molelcules
Total (without water)21,9231
Polymers21,9231
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)52 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Interleukin-6 / IL-6 / Interleukin HP-1 / B-cell hybridoma growth factor


Mass: 21922.924 Da / Num. of mol.: 1 / Fragment: unp residues 27-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il6, Il-6 / Production host: Escherichia coli (E. coli) / References: UniProt: P08505

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1342D 1H-1H TOCSY
1442D 1H-1H NOESY
1523D CBCA(CO)NH
1623D HN(CA)CB
1723D HNCO
1833D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-15N TOCSY
11143D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1430 uM [U-100% 15N] IL-6, 95% H2O/5% D2O95% H2O/5% D2O
2350 uM [U-100% 13C; U-100% 15N] IL-6, 95% H2O/5% D2O95% H2O/5% D2O
3350 uM [U-100% 13C; U-100% 15N] IL-6, 100% D2O100% D2O
4400 uM IL-6, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
430 uMIL-6-1[U-100% 15N]1
350 uMIL-6-2[U-100% 13C; U-100% 15N]2
350 uMIL-6-3[U-100% 13C; U-100% 15N]3
400 uMIL-6-44
Sample conditionsIonic strength: 100 / pH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceBrukerAvance8002

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Processing

NMR software
NameDeveloperClassification
TOPSPINBruker Biospincollection
TOPSPINBruker Biospinprocessing
SPARKYGoddarddata analysis
SPARKYGoddardchemical shift assignment
SPARKYGoddardpeak picking
MolmolKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 52

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