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- PDB-2il6: HUMAN INTERLEUKIN-6, NMR, 32 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 2il6
TitleHUMAN INTERLEUKIN-6, NMR, 32 STRUCTURES
ComponentsINTERLEUKIN-6
KeywordsCYTOKINE / GLYCOPROTEIN / GROWTH FACTOR
Function / homology
Function and homology information


regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / regulation of glucagon secretion / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / germinal center B cell differentiation / interleukin-6 receptor complex ...regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / regulation of glucagon secretion / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / germinal center B cell differentiation / interleukin-6 receptor complex / positive regulation of apoptotic DNA fragmentation / positive regulation of type B pancreatic cell apoptotic process / positive regulation of extracellular matrix disassembly / hepatocyte proliferation / regulation of microglial cell activation / response to peptidoglycan / neutrophil apoptotic process / interleukin-6 receptor binding / positive regulation of B cell activation / positive regulation of receptor signaling pathway via STAT / inflammatory response to wounding / T-helper 17 cell lineage commitment / positive regulation of T-helper 2 cell cytokine production / negative regulation of collagen biosynthetic process / endocrine pancreas development / positive regulation of acute inflammatory response / regulation of neuroinflammatory response / vascular endothelial growth factor production / negative regulation of chemokine production / T follicular helper cell differentiation / positive regulation of neuroinflammatory response / positive regulation of leukocyte chemotaxis / cell surface receptor signaling pathway via STAT / neutrophil mediated immunity / positive regulation of cytokine production involved in inflammatory response / positive regulation of platelet aggregation / negative regulation of bone resorption / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / positive regulation of immunoglobulin production / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / maintenance of blood-brain barrier / negative regulation of fat cell differentiation / MAPK3 (ERK1) activation / monocyte chemotaxis / MAPK1 (ERK2) activation / Interleukin-10 signaling / positive regulation of interleukin-17 production / humoral immune response / positive regulation of interleukin-10 production / Transcriptional Regulation by VENTX / negative regulation of lipid storage / positive regulation of vascular endothelial growth factor production / cell surface receptor signaling pathway via JAK-STAT / regulation of angiogenesis / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / response to glucocorticoid / positive regulation of T cell proliferation / positive regulation of chemokine production / positive regulation of glial cell proliferation / regulation of insulin secretion / liver regeneration / positive regulation of translation / positive regulation of interleukin-1 beta production / cytokine activity / acute-phase response / response to activity / positive regulation of interleukin-8 production / positive regulation of DNA-binding transcription factor activity / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of smooth muscle cell proliferation / Post-translational protein phosphorylation / growth factor activity / positive regulation of peptidyl-serine phosphorylation / cytokine-mediated signaling pathway / positive regulation of miRNA transcription / platelet activation / negative regulation of neurogenesis / positive regulation of interleukin-6 production / cellular response to virus / cellular response to hydrogen peroxide / neuron cellular homeostasis / neuron projection development / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of peptidyl-tyrosine phosphorylation / ADORA2B mediated anti-inflammatory cytokines production / positive regulation of tumor necrosis factor production / glucose homeostasis / cellular response to lipopolysaccharide / Senescence-Associated Secretory Phenotype (SASP) / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / defense response to virus / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / positive regulation of apoptotic process / inflammatory response / endoplasmic reticulum lumen
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING.
AuthorsXu, G.Y. / Yu, H.A. / Hong, J. / Stahl, M. / Mcdonagh, T. / Kay, L.E. / Cumming, D.A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Solution structure of recombinant human interleukin-6.
Authors: Xu, G.Y. / Yu, H.A. / Hong, J. / Stahl, M. / McDonagh, T. / Kay, L.E. / Cumming, D.A.
#1: Journal: J.Biomol.NMR / Year: 1996
Title: Complete 1H, 15N and 13C Assignments, Secondary Structure, and Topology of Recombinant Human Interleukin-6
Authors: Xu, G.Y. / Hong, J. / Mcdonagh, T. / Stahl, M. / Kay, L.E. / Seehra, J. / Cumming, D.A.
History
DepositionJan 31, 1997Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)21,0061
Polymers21,0061
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)32 / 75LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein INTERLEUKIN-6


Mass: 21005.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05231
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112/3/4D NOESY
121TOCSY
131ETC.

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Sample preparation

Sample conditionspH: 6.1 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY PLUS 600 / Manufacturer: Varian / Model: UNITY PLUS 600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING. / Software ordinal: 1
Details: STRUCTURES ARE BASED ON 2961 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NMR MEASUREMENTS INCLUDING 138 HYDROGEN BOND RESTRAINTS FROM 69 HYDROGEN BONDS IDENTIFIED USING AMIDE EXCHANGE DATA ...Details: STRUCTURES ARE BASED ON 2961 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NMR MEASUREMENTS INCLUDING 138 HYDROGEN BOND RESTRAINTS FROM 69 HYDROGEN BONDS IDENTIFIED USING AMIDE EXCHANGE DATA AND INITIAL STRUCTURE CALCULATIONS. IN ADDITION, 83 PHI BACKBONE TORSION ANGLE RESTRAINTS WERE DERIVED FROM COUPLING CONSTANTS. THE METHOD USED TO DERIVE THE FINAL ENSEMBLE OF STRUCTURES IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (M. NILGES, G.M. CLORE, AND A.M. GRONENBORN (1988) FEBS LETT. 229, 317-324.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 75 / Conformers submitted total number: 32

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