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- SASDAY7: IL-6R tetramer-dimer equilibrium (Interleukin-6 receptor subunit ... -
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Open data
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Basic information
Entry | Database: SASBDB / ID: SASDAY7 |
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![]() | IL-6R tetramer-dimer equilibrium
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Function / homology | ![]() ciliary neurotrophic factor binding / interleukin-6 receptor activity / interleukin-6 binding / hepatic immune response / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor-mediated signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-6 receptor complex / negative regulation of collagen biosynthetic process ...ciliary neurotrophic factor binding / interleukin-6 receptor activity / interleukin-6 binding / hepatic immune response / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor-mediated signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-6 receptor complex / negative regulation of collagen biosynthetic process / : / T-helper 17 cell lineage commitment / endocrine pancreas development / positive regulation of glomerular mesangial cell proliferation / negative regulation of interleukin-8 production / vascular endothelial growth factor production / positive regulation of leukocyte chemotaxis / neutrophil mediated immunity / cytokine receptor activity / interleukin-6-mediated signaling pathway / Interleukin-6 signaling / MAPK3 (ERK1) activation / monocyte chemotaxis / MAPK1 (ERK2) activation / positive regulation of osteoblast differentiation / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / positive regulation of tyrosine phosphorylation of STAT protein / response to cytokine / acute-phase response / positive regulation of smooth muscle cell proliferation / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / 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 |
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![]() | ![]() Title: Structure and target interaction of a G-quadruplex RNA-aptamer. Authors: Kristina Szameit / Katharina Berg / Sven Kruspe / Erica Valentini / Eileen Magbanua / Marcel Kwiatkowski / Isaure Chauvot de Beauchêne / Boris Krichel / Kira Schamoni / Charlotte Uetrecht / ...Authors: Kristina Szameit / Katharina Berg / Sven Kruspe / Erica Valentini / Eileen Magbanua / Marcel Kwiatkowski / Isaure Chauvot de Beauchêne / Boris Krichel / Kira Schamoni / Charlotte Uetrecht / Dmitri I Svergun / Hartmut Schlüter / Martin Zacharias / Ulrich Hahn / ![]() Abstract: G-quadruplexes have recently moved into focus of research in nucleic acids, thereby evolving in scientific significance from exceptional secondary structure motifs to complex modulators of gene ...G-quadruplexes have recently moved into focus of research in nucleic acids, thereby evolving in scientific significance from exceptional secondary structure motifs to complex modulators of gene regulation. Aptamers (nucleic acid based ligands with recognition properties for a specific target) that form Gquadruplexes may have particular potential for therapeutic applications as they combine the characteristics of specific targeting and Gquadruplex mediated stability and regulation. We have investigated the structure and target interaction properties of one such aptamer: AIR-3 and its truncated form AIR-3A. These RNA aptamers are specific for human interleukin-6 receptor (hIL-6R), a key player in inflammatory diseases and cancer, and have recently been exploited for in vitro drug delivery studies. With the aim to resolve the RNA structure, global shape, RNA:protein interaction site and binding stoichiometry, we now investigated AIR-3 and AIR-3A by different methods including RNA structure probing, Small Angle X-ray scattering and microscale thermophoresis. Our findings suggest a broader spectrum of folding species than assumed so far and remarkable tolerance toward different modifications. Mass spectrometry based binding site analysis, supported by molecular modeling and docking studies propose a general Gquadruplex affinity for the target molecule hIL-6R. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
-Data source
SASBDB page | ![]() |
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-Related structure data
Related structure data | C: citing same article ( |
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Similar structure data |
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External links
Related items in Molecule of the Month |
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-Models
Model #300 | ![]() Type: mix / Software: CORAL / Chi-square value: 2.49 ![]() |
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Model #301 | ![]() Type: mix / Software: CORAL-OLIGOMER / Radius of dummy atoms: 1.90 A / Chi-square value: 1.33 ![]() |
Model #302 | ![]() Type: mix / Software: CORAL-OLIGOMER / Radius of dummy atoms: 1.90 A / Comment: extended dimer / Chi-square value: 1.33 ![]() |
Model #303 | ![]() Type: mix / Software: CORAL-OLIGOMER / Radius of dummy atoms: 1.90 A / Chi-square value: 1.92 ![]() |
Model #304 | ![]() Type: mix / Software: CORAL-OLIGOMER / Comment: compact dimer / Chi-square value: 1.92 ![]() |
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Sample
![]() | Name: IL-6R tetramer-dimer equilibrium / Specimen concentration: 0.1 mg/ml / Entity id: 171 / 174 |
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Buffer | Name: water / pH: 7.5 |
Entity #171 | Name: IL-6R / Type: protein / Description: Interleukin-6 receptor subunit alpha / Formula weight: 40.964 / Num. of mol.: 4 / Source: Homo sapiens / References: UniProt: P08887 Sequence: MRAWIFFLLC LAGRALAAPL VHHHHHHALA PRRCPAQEVA RGVLTSLPGD SVTLTCPGVE PEDNATVHWV LRKPAAGSHP SRWAGMGRRL LLRSVQLHDS GNYSCYRAGR PAGTVHLLVD VPPEEPQLSC FRKSPLSNVV CEWGPRSTPS LTTKAVLLVR KFQNSPAEDF ...Sequence: MRAWIFFLLC LAGRALAAPL VHHHHHHALA PRRCPAQEVA RGVLTSLPGD SVTLTCPGVE PEDNATVHWV LRKPAAGSHP SRWAGMGRRL LLRSVQLHDS GNYSCYRAGR PAGTVHLLVD VPPEEPQLSC FRKSPLSNVV CEWGPRSTPS LTTKAVLLVR KFQNSPAEDF QEPCQYSQES QKFSCQLAVP EGDSSFYIVS MCVASSVGSK FSKTQTFQGC GILQPDPPAN ITVTAVARNP RWLSVTWQDP HSWNSSFYRL RFELRYRAER SKTFTTWMVK DLQHHCVIHD AWSGLRHVVQ LRAQEEFGQG EWSEWSPEAM GTPWTESRSP PAENEVSTPM QALTTNKDDD NILFRDSANA TSLPVQ |
Entity #174 | Name: IL-6R / Type: protein / Description: Interleukin-6 receptor subunit alpha / Formula weight: 40.964 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: P08887 Sequence: MRAWIFFLLC LAGRALAAPL VHHHHHHALA PRRCPAQEVA RGVLTSLPGD SVTLTCPGVE PEDNATVHWV LRKPAAGSHP SRWAGMGRRL LLRSVQLHDS GNYSCYRAGR PAGTVHLLVD VPPEEPQLSC FRKSPLSNVV CEWGPRSTPS LTTKAVLLVR KFQNSPAEDF ...Sequence: MRAWIFFLLC LAGRALAAPL VHHHHHHALA PRRCPAQEVA RGVLTSLPGD SVTLTCPGVE PEDNATVHWV LRKPAAGSHP SRWAGMGRRL LLRSVQLHDS GNYSCYRAGR PAGTVHLLVD VPPEEPQLSC FRKSPLSNVV CEWGPRSTPS LTTKAVLLVR KFQNSPAEDF QEPCQYSQES QKFSCQLAVP EGDSSFYIVS MCVASSVGSK FSKTQTFQGC GILQPDPPAN ITVTAVARNP RWLSVTWQDP HSWNSSFYRL RFELRYRAER SKTFTTWMVK DLQHHCVIHD AWSGLRHVVQ LRAQEEFGQG EWSEWSPEAM GTPWTESRSP PAENEVSTPM QALTTNKDDD NILFRDSANA TSLPVQ |
-Experimental information
Beam | Instrument name: Diamond Light Source B21 / City: Oxfordshire / 国: UK ![]() | |||||||||||||||||||||||||||||||||
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Detector | Name: Pilatus 2M | |||||||||||||||||||||||||||||||||
Scan |
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Distance distribution function P(R) |
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Result | Comments: The curve was fitted with a tetramer obtained with CORAL from the unit cell tetrameric structure of the pdb code 1N26 with a Chi-squared-value of 2.49. Since the experimental MW appeared ...Comments: The curve was fitted with a tetramer obtained with CORAL from the unit cell tetrameric structure of the pdb code 1N26 with a Chi-squared-value of 2.49. Since the experimental MW appeared smaller than a tetramer (confirmed by a not-fitting tetrameric model) we tried to fit a mixture of tetramer-dimer using OLIGOMER. Two possible dimers were possible: a compact and an extended one. With the compact dimer mixture OLIGOMER estimated a volume fraction of 65% tetramer and 35% dimer and a corresponding Chi-squared-value of 1.92. With the extended dimer mixture OLIGOMER estimated a volume fraction of 47% tetramer and 53% dimer and a improved Chi-squared-value of 1.33.
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