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データを開く
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基本情報
登録情報 | データベース: SASBDB / ID: SASDAY7 |
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![]() | IL-6R tetramer-dimer equilibrium
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機能・相同性 | ![]() 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 類似検索 - 分子機能 |
生物種 | ![]() |
![]() | ![]() タイトル: Structure and target interaction of a G-quadruplex RNA-aptamer. 著者: Kristina Szameit / Katharina Berg / Sven Kruspe / Erica Valentini / Eileen Magbanua / Marcel Kwiatkowski / Isaure Chauvot de Beauchêne / Boris Krichel / Kira Schamoni / Charlotte Uetrecht / ...著者: 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 / ![]() 要旨: 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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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
-モデル
モデル #300 | ![]() タイプ: mix / ソフトウェア: CORAL / カイ2乗値: 2.49 ![]() |
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モデル #301 | ![]() タイプ: mix / ソフトウェア: CORAL-OLIGOMER / ダミー原子の半径: 1.90 A / カイ2乗値: 1.33 ![]() |
モデル #302 | ![]() タイプ: mix / ソフトウェア: CORAL-OLIGOMER / ダミー原子の半径: 1.90 A / コメント: extended dimer / カイ2乗値: 1.33 ![]() |
モデル #303 | ![]() タイプ: mix / ソフトウェア: CORAL-OLIGOMER / ダミー原子の半径: 1.90 A / カイ2乗値: 1.92 ![]() |
モデル #304 | ![]() タイプ: mix / ソフトウェア: CORAL-OLIGOMER / コメント: compact dimer / カイ2乗値: 1.92 ![]() |
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試料
![]() | 名称: IL-6R tetramer-dimer equilibrium / 試料濃度: 0.1 mg/ml / Entity id: 171 / 174 |
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バッファ | 名称: water / pH: 7.5 |
要素 #171 | 名称: IL-6R / タイプ: protein / 記述: Interleukin-6 receptor subunit alpha / 分子量: 40.964 / 分子数: 4 / 由来: Homo sapiens / 参照: UniProt: P08887 配列: MRAWIFFLLC LAGRALAAPL VHHHHHHALA PRRCPAQEVA RGVLTSLPGD SVTLTCPGVE PEDNATVHWV LRKPAAGSHP SRWAGMGRRL LLRSVQLHDS GNYSCYRAGR PAGTVHLLVD VPPEEPQLSC FRKSPLSNVV CEWGPRSTPS LTTKAVLLVR KFQNSPAEDF ...配列: 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 |
要素 #174 | 名称: IL-6R / タイプ: protein / 記述: Interleukin-6 receptor subunit alpha / 分子量: 40.964 / 分子数: 2 / 由来: Homo sapiens / 参照: UniProt: P08887 配列: MRAWIFFLLC LAGRALAAPL VHHHHHHALA PRRCPAQEVA RGVLTSLPGD SVTLTCPGVE PEDNATVHWV LRKPAAGSHP SRWAGMGRRL LLRSVQLHDS GNYSCYRAGR PAGTVHLLVD VPPEEPQLSC FRKSPLSNVV CEWGPRSTPS LTTKAVLLVR KFQNSPAEDF ...配列: 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 |
-実験情報
ビーム | 設備名称: Diamond Light Source B21 / 地域: Oxfordshire / 国: UK ![]() | |||||||||||||||||||||||||||||||||
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検出器 | 名称: Pilatus 2M | |||||||||||||||||||||||||||||||||
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距離分布関数 P(R) |
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結果 | コメント: 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 ...コメント: 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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