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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: 1mi5 | ||||||
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タイトル | The crystal structure of LC13 TcR in complex with HLAB8-EBV peptide complex | ||||||
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![]() | IMMUNE SYSTEM / T cell receptor / Major histocompatability complex (class I) / HLA B8 / Epstein Barr Virus / Immunodominant TcR (LC13) | ||||||
機能・相同性 | ![]() host cell nuclear matrix / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules ...host cell nuclear matrix / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / TAP binding / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / detection of bacterium / immunoglobulin complex, circulating / immunoglobulin receptor binding / viral process / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / complement activation, classical pathway / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen binding / response to bacterium / 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 / ER to Golgi transport vesicle membrane / 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 / defense response / 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 / specific granule lumen / recycling endosome membrane / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / Downstream TCR signaling / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / protein-folding chaperone binding / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / blood microparticle / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding 類似検索 - 分子機能 | ||||||
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手法 | ![]() ![]() ![]() | ||||||
![]() | Kjer-Nielsen, L. / Clements, C.S. / Purcell, A.W. / Brooks, A.G. / Whisstock, J.C. / Burrows, S.R. / McCluskey, J. / Rossjohn, J. | ||||||
![]() | ![]() タイトル: A Structural Basis for the Selection of Dominant alphabeta T Cell Receptors in Antiviral Immunity 著者: Kjer-Nielsen, L. / Clements, C.S. / Purcell, A.W. / Brooks, A.G. / Whisstock, J.C. / Burrows, S.R. / McCluskey, J. / Rossjohn, J. | ||||||
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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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ダウンロード
PDBx/mmCIF形式 | ![]() | 180.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 142.5 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 | ![]() | 393.4 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 410.7 KB | 表示 | |
XML形式データ | ![]() | 18.8 KB | 表示 | |
CIF形式データ | ![]() | 29.5 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 | |
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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 , 3種, 3分子 BDE
#2: タンパク質 | 分子量: 11748.160 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#4: タンパク質 | 分子量: 22317.717 Da / 分子数: 1 / 断片: extracellular domain / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#5: タンパク質 | 分子量: 27153.035 Da / 分子数: 1 / 断片: extracellular domain / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
-抗体 / タンパク質・ペプチド / 非ポリマー , 3種, 234分子 AC![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: 抗体 | 分子量: 32015.055 Da / 分子数: 1 / 断片: extracellular domain / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#3: タンパク質・ペプチド | 分子量: 1054.247 Da / 分子数: 1 / 断片: nonamer peptide / 由来タイプ: 合成 詳細: Epstein barr Virus peptide was chemically synthesized. 参照: GenBank: 242890, UniProt: Q3KST2*PLUS |
#6: 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: 2.29 Å3/Da / 溶媒含有率: 46.31 % | ||||||||||||||||||
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: PEG, ammonium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||
結晶化 | *PLUS | ||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2002年4月7日 |
放射 | 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: 1 Å / 相対比: 1 |
反射 | 解像度: 2.5→50 Å / Num. all: 29027 / Num. obs: 77349 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 2.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.1 |
反射 シェル | 解像度: 2.5→2.6 Å / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.4 / % possible all: 95 |
反射 | *PLUS 最低解像度: 50 Å / Num. obs: 29027 / Num. measured all: 77349 |
反射 シェル | *PLUS % possible obs: 95 % |
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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: the unliganded components 解像度: 2.5→50 Å / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
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精密化ステップ | サイクル: LAST / 解像度: 2.5→50 Å
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精密化 | *PLUS 最低解像度: 50 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS | |||||||||||||||||||||||||
拘束条件 | *PLUS
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