+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7ndq | ||||||
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タイトル | Gag:02 TCR in complex with HLA-E. | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / TCR-pHLA complex / non-natural amino acid | ||||||
機能・相同性 | 機能・相同性情報 MHC protein binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding ...MHC protein binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / T cell activation involved in immune response / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / T cell receptor complex / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / viral budding via host ESCRT complex / MHC class I protein binding / Generation of second messenger molecules / PD-1 signaling / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / 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 / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / Downstream TCR signaling / 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 differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / antibacterial humoral response / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / 獲得免疫系 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.551 Å | ||||||
データ登録者 | Pengelly, R.J. / Robinson, R.A. | ||||||
引用 | ジャーナル: Eur.J.Immunol. / 年: 2022 タイトル: Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition. 著者: Barber, C. / De Souza, V.A. / Paterson, R.L. / Martin-Urdiroz, M. / Mulakkal, N.C. / Srikannathasan, V. / Connolly, M. / Phillips, G. / Foong-Leong, T. / Pengelly, R. / Karuppiah, V. / Grant, ...著者: Barber, C. / De Souza, V.A. / Paterson, R.L. / Martin-Urdiroz, M. / Mulakkal, N.C. / Srikannathasan, V. / Connolly, M. / Phillips, G. / Foong-Leong, T. / Pengelly, R. / Karuppiah, V. / Grant, T. / Dembek, M. / Verma, A. / Gibbs-Howe, D. / Blicher, T.H. / Knox, A. / Robinson, R.A. / Cole, D.K. / Leonard, S. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7ndq.cif.gz | 325.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7ndq.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 7ndq.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/nd/7ndq ftp://data.pdbj.org/pub/pdb/validation_reports/nd/7ndq | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
-タンパク質 , 4種, 4分子 AAABBBDDDEEE
#1: タンパク質 | 分子量: 31955.203 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-E, HLA-6.2, HLAE / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P13747 |
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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) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61769 |
#4: タンパク質 | 分子量: 22074.508 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRAV4, TRAJ23, TRA / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: A0A0B4J268, UniProt: A0A075B6U7, UniProt: P0DSE1 |
#5: タンパク質 | 分子量: 27913.975 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRBV7-9, TRBJ1-2, B2M, HDCMA22P / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: P04435, UniProt: A0A0J9YX06, UniProt: K7N5M4 |
-タンパク質・ペプチド / 非ポリマー , 2種, 14分子 CCC
#3: タンパク質・ペプチド | 分子量: 1066.295 Da / 分子数: 1 / 由来タイプ: 合成 由来: (合成) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) 参照: UniProt: B6S6I4 |
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#6: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 3.07 Å3/Da / 溶媒含有率: 59.88 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 23.2% (w/v) PEG 1500, 93 mM MMT pH 9.0 |
-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: シンクロトロン / サイト: Diamond / ビームライン: I04 / 波長: 0.9795 Å |
検出器 | タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2020年12月2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: 0.9795 Å / 相対比: 1 |
反射 | 解像度: 2.55→85.354 Å / Num. obs: 39941 / % possible obs: 100 % / 冗長度: 26.3 % / CC1/2: 1 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.041 / Net I/σ(I): 11.6 |
反射 シェル | 解像度: 2.55→2.59 Å / Rmerge(I) obs: 6.926 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1932 / CC1/2: 0.735 / Rpim(I) all: 1.343 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 5W1W, 5EU6 解像度: 2.551→76.445 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.197 / SU B: 50.437 / SU ML: 0.424 / Average fsc free: 0.7878 / Average fsc work: 0.8046 / 交差検証法: FREE R-VALUE / ESU R: 0.468 / ESU R Free: 0.32 / 詳細: Hydrogens have been added in their riding positions
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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 / 溶媒モデル: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 90.49 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.551→76.445 Å
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拘束条件 |
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LS精密化 シェル |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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