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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: 7n5c | ||||||
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タイトル | 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond | ||||||
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![]() | IMMUNE SYSTEM / Major Histocompatibility complex / MHC / mouse / Influenza A / polymerase acidic protein / H2Db / T cell receptor / PA224-233 / disulfide bond / Cysteine | ||||||
機能・相同性 | ![]() cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / 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 ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / 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 / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / cellular response to iron(III) ion / peptide binding / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / endonuclease activity / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / 加水分解酵素; エステル加水分解酵素 / learning or memory / cell surface receptor signaling pathway / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / viral RNA genome replication / lysosomal membrane / focal adhesion / signaling receptor binding / DNA-templated transcription / host cell nucleus / Neutrophil degranulation / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Szeto, C. / Gras, S. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus. 著者: Szeto, C. / Zareie, P. / Wirasinha, R.C. / Zhang, J.B. / Nguyen, A.T. / Riboldi-Tunnicliffe, A. / La Gruta, N.L. / Gras, S. / Daley, S.R. | ||||||
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 | ![]() | 187.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 143.9 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
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アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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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: 32174.781 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() 発現宿主: ![]() ![]() 参照: UniProt: P01899 |
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#2: タンパク質 | 分子量: 11879.356 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P61769 |
-タンパク質・ペプチド , 1種, 1分子 C
#3: タンパク質・ペプチド | 分子量: 1160.324 Da / 分子数: 1 / Mutation: E4C / 由来タイプ: 合成 詳細: Polymerase Acidic Protein 224-233 with E227C (E4C) mutation 由来: (合成) ![]() ![]() 参照: UniProt: O89752 |
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-Fusion protein of T cell receptor ... , 2種, 2分子 DE
#4: タンパク質 | 分子量: 22510.906 Da / 分子数: 1 / Mutation: S110C / 由来タイプ: 組換発現 / 詳細: 6218 TCR-alpha with S110C mutation 由来: (組換発現) ![]() ![]() ![]() 遺伝子: Trav21-dv12 発現宿主: ![]() ![]() 参照: UniProt: A0A075B6C4, UniProt: K7N5N2 |
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#5: タンパク質 | 分子量: 27575.906 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: 6218 TCR beta chain 由来: (組換発現) ![]() ![]() ![]() 遺伝子: Trbv29, B2M, HDCMA22P 発現宿主: ![]() ![]() 参照: UniProt: A0A0G2LB96, UniProt: K7N5M4 |
-非ポリマー , 2種, 262分子 ![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: 化合物 | ChemComp-NA / |
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#7: 水 | ChemComp-HOH / |
-詳細
研究の焦点であるリガンドがあるか | N |
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-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: 2.53 Å3/Da / 溶媒含有率: 51.34 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法 詳細: 20% PEG3350, 0.2M NaF, 0.05M NaForm, 1% 1,5-Diaminopentane dihydrochloride |
-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 EIGER X 16M / 検出器: PIXEL / 日付: 2020年7月28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: 0.987 Å / 相対比: 1 | ||||||||||||||||||||||||||||||
反射 | 解像度: 1.87→47.41 Å / Num. obs: 77867 / % possible obs: 100 % / 冗長度: 7 % / Biso Wilson estimate: 35.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Net I/σ(I): 12.9 / Num. measured all: 546387 / Scaling rejects: 744 | ||||||||||||||||||||||||||||||
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: 3PQY 解像度: 1.87→27.14 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.141 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.129
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原子変位パラメータ | Biso max: 132.21 Å2 / Biso mean: 41.79 Å2 / Biso min: 12.46 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 1.87→27.14 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.87→1.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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