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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: PDB / ID: 6ojp | |||||||||
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タイトル | Structure of glycolipid alpha-GSA[8,6P] in complex with mouse CD1d | |||||||||
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![]() | IMMUNE SYSTEM / glycolipid-antigen presentation / MHC-fold / IG-fold | |||||||||
機能・相同性 | ![]() regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-4 production / antigen processing and presentation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of type II interferon production / sensory perception of smell / late endosome / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / lysosome / early endosome / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Zajonc, D.M. / Bitra, A. | |||||||||
![]() | ![]() タイトル: A molecular switch in mouse CD1d modulates natural killer T cell activation by alpha-galactosylsphingamides. 著者: Wang, J. / Guillaume, J. / Janssens, J. / Remesh, S.G. / Ying, G. / Bitra, A. / Van Calenbergh, S. / Zajonc, D.M. | |||||||||
履歴 |
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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
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PDBx/mmCIF形式 | ![]() | 102.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 73.4 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.5 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.5 MB | 表示 | |
XML形式データ | ![]() | 17.6 KB | 表示 | |
CIF形式データ | ![]() | 23.7 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 6c5mC ![]() 6c69C ![]() 6c6aC ![]() 6c6cC ![]() 6c6eC ![]() 6c6hC ![]() 6c6jC ![]() 6cw6C ![]() 6cw9C ![]() 6cwbC ![]() 6cx5C ![]() 6cx7C ![]() 6cx9C ![]() 6cxaC ![]() 6cxeC ![]() 6cxfC ![]() 2q7yS S: 精密化の開始モデル C: 同じ文献を引用 ( |
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類似構造データ |
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
-タンパク質 , 2種, 2分子 AB
#1: タンパク質 | 分子量: 32607.641 Da / 分子数: 1 / 断片: UNP residues 19-297 / 変異: Y73H / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() 発現宿主: ![]() ![]() 参照: UniProt: A0A0R4J090, UniProt: P11609*PLUS |
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#2: タンパク質 | 分子量: 11660.350 Da / 分子数: 1 / 断片: UNP residues 21-119 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() 発現宿主: ![]() ![]() 参照: UniProt: P01887 |
-糖 , 3種, 4分子 ![](data/chem/img/NAG.gif)
#3: 多糖 | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose |
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#4: 多糖 | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#5: 糖 |
-非ポリマー , 5種, 91分子 ![](data/chem/img/7LP.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#6: 化合物 | ChemComp-7LP / ( | ||||
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#7: 化合物 | ChemComp-PLM / | ||||
#8: 化合物 | ChemComp-GOL / #9: 化合物 | ChemComp-SO4 / | #10: 水 | ChemComp-HOH / | |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.67 Å3/Da / 溶媒含有率: 53.85 % |
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 20% PEG3350, 8% Tacsimate, pH 4.0 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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放射光源 | 由来: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2015年5月28日 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
放射 | モノクロメーター: Si(111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
放射波長 | 波長: 0.976 Å / 相対比: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 2.17→40 Å / Num. obs: 23559 / % possible obs: 89.9 % / 冗長度: 4.1 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.041 / Rrim(I) all: 0.09 / Χ2: 1.154 / Net I/σ(I): 9.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB entry 2Q7Y 解像度: 2.17→36.61 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.038 / SU ML: 0.17 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.217 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 85.46 Å2 / Biso mean: 35.495 Å2 / Biso min: 22.36 Å2
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精密化ステップ | サイクル: final / 解像度: 2.17→36.61 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.17→2.226 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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