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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 / negative regulation of muscle organ development / negative regulation of membrane potential / glucagon secretion / positive regulation of interleukin-21 production / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / regulation of glucagon secretion / hepatic immune response / Interleukin-6 signaling ...positive regulation of gliogenesis / negative regulation of muscle organ development / negative regulation of membrane potential / glucagon secretion / positive regulation of interleukin-21 production / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / regulation of glucagon secretion / hepatic immune response / Interleukin-6 signaling / negative regulation of primary miRNA processing / regulation of vascular endothelial growth factor production / negative regulation of interleukin-1-mediated signaling pathway / positive regulation of transmission of nerve impulse / positive regulation of cell proliferation in bone marrow / interleukin-6 receptor complex / positive regulation of apoptotic DNA fragmentation / hepatocyte proliferation / 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 / germinal center B cell differentiation / neutrophil apoptotic process / positive regulation of extracellular matrix disassembly / positive regulation of T-helper 2 cell differentiation / positive regulation of B cell activation / positive regulation of receptor signaling pathway via STAT / cellular response to interleukin-17 / interleukin-6 receptor binding / regulation of circadian sleep/wake cycle, non-REM sleep / T-helper 17 cell lineage commitment / positive regulation of T-helper 2 cell cytokine production / inflammatory response to wounding / endocrine pancreas development / epithelial cell proliferation involved in salivary gland morphogenesis / negative regulation of collagen biosynthetic process / positive regulation of acute inflammatory response / vascular endothelial growth factor production / negative regulation of chemokine production / T follicular helper cell differentiation / branching involved in salivary gland morphogenesis / positive regulation of platelet aggregation / cell surface receptor signaling pathway via STAT / positive regulation of cytokine production involved in inflammatory response / negative regulation of bone resorption / myeloid cell homeostasis / positive regulation of leukocyte adhesion to vascular endothelial cell / cellular response to hepatocyte growth factor stimulus / interleukin-6-mediated signaling pathway / positive regulation of immunoglobulin production / muscle cell cellular homeostasis / defense response to protozoan / positive regulation of interleukin-17 production / regulation of insulin secretion / histone H3K9ac reader activity / positive regulation of interleukin-10 production / positive regulation of glial cell proliferation / positive regulation of vascular endothelial growth factor production / negative regulation of gluconeogenesis / cellular response to interleukin-1 / positive regulation of epithelial to mesenchymal transition / cell surface receptor signaling pathway via JAK-STAT / positive regulation of chemokine production / positive regulation of neuron differentiation / positive regulation of T cell proliferation / liver regeneration / cell redox homeostasis / positive regulation of smooth muscle cell proliferation / response to glucocorticoid / positive regulation of DNA replication / cytokine activity / positive regulation of epithelial cell proliferation / T cell activation / acute-phase response / response to activity / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / response to amphetamine / positive regulation of translation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of neuron projection development / cellular response to virus / positive regulation of protein import into nucleus / positive regulation of interleukin-6 production / positive regulation of miRNA transcription / response to wounding / cellular response to tumor necrosis factor / cellular response to hydrogen peroxide / cytokine-mediated signaling pathway / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / neuron projection development / regulation of cell shape / regulation of cell population proliferation / glucose homeostasis / cellular response to lipopolysaccharide / regulation of apoptotic process / gene expression / defense response to virus
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
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / 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-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
Has protein modificationY

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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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