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- PDB-2arw: The solution structure of the membrane proximal cytokine receptor... -

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Basic information

Entry
Database: PDB / ID: 2arw
TitleThe solution structure of the membrane proximal cytokine receptor domain of the human interleukin-6 receptor
ComponentsInterleukin-6 receptor alpha chain
KeywordsCYTOKINE / fibronectin-type III like
Function / homology
Function and homology information


ciliary neurotrophic factor binding / interleukin-6 receptor activity / interleukin-6 binding / hepatic immune response / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor receptor complex / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / positive regulation of activation of Janus kinase activity ...ciliary neurotrophic factor binding / interleukin-6 receptor activity / interleukin-6 binding / hepatic immune response / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor receptor complex / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / positive regulation of activation of Janus kinase activity / negative regulation of collagen biosynthetic process / T-helper 17 cell lineage commitment / positive regulation of glomerular mesangial cell proliferation / endocrine pancreas development / negative regulation of interleukin-8 production / vascular endothelial growth factor production / positive regulation of leukocyte chemotaxis / neutrophil mediated immunity / cytokine receptor activity / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / MAPK3 (ERK1) activation / monocyte chemotaxis / MAPK1 (ERK2) activation / positive regulation of osteoblast differentiation / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / response to cytokine / acute-phase response / positive regulation of smooth muscle cell proliferation / positive regulation of interleukin-6 production / cytokine-mediated signaling pathway / Transcriptional regulation of granulopoiesis / positive regulation of peptidyl-tyrosine phosphorylation / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / Potential therapeutics for SARS / positive regulation of MAPK cascade / receptor complex / defense response to Gram-positive bacterium / apical plasma membrane / external side of plasma membrane / positive regulation of cell population proliferation / enzyme binding / protein homodimerization activity / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Interleukin-6 receptor alpha chain, binding / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin / Immunoglobulin domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. ...Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Interleukin-6 receptor alpha chain, binding / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin / Immunoglobulin domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-6 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamicsu
Model type detailsminimized average
AuthorsHecht, O. / Dingley, A.J. / Schwantner, A. / Ozbek, S. / Rose-John, S. / Grotzinger, J.
CitationJournal: Biol.Chem. / Year: 2006
Title: The solution structure of the membrane-proximal cytokine receptor domain of the human interleukin-6 receptor
Authors: Hecht, O. / Dingley, A.J. / Schwanter, A. / Ozbek, S. / Rose-John, S. / Grotzinger, J.
History
DepositionAug 22, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-6 receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)14,6801
Polymers14,6801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein Interleukin-6 receptor alpha chain / IL-6R-alpha / IL-6R 1 / CD126 antigen


Mass: 14680.381 Da / Num. of mol.: 1 / Fragment: Third extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSET 5b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08887

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CBCA(CO)NH
121CBCANH
131HNCA
1413D 15N-separated NOESY
151HBHA(CBCACO)NH
1613D 13C-separated NOESY

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Sample preparation

DetailsContents: 20mM phosphatebuffer pH 5.0, 95% H2O, 5% D2O / Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 50mM phosphate / pH: 5.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
DYANA1.5Guentertrefinement
RefinementMethod: torsion angle dynamicsu / Software ordinal: 1
Details: The structures is based on a total of 932 NOE-derived distance restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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