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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: 5nqk | ||||||
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タイトル | human 199.16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2 | ||||||
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![]() | IMMUNE SYSTEM / Melan-A/MART-1 PEPTIDE / DECAPEPTIDE / MHC CLASS I / HLA-A2 / T cell receptor | ||||||
機能・相同性 | ![]() melanosome membrane / alpha-beta T cell receptor complex / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / T cell receptor complex ...melanosome membrane / alpha-beta T cell receptor complex / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / T cell receptor complex / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / Regulation of MITF-M-dependent genes involved in pigmentation / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / 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 / immune system process / detection of bacterium / T cell receptor binding / endomembrane system / : / : / negative regulation of receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / peptide antigen assembly with MHC class II protein complex / trans-Golgi network / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / positive regulation of protein binding / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / antibacterial humoral response / melanosome / tertiary granule lumen / DAP12 signaling / Downstream TCR signaling / T cell differentiation in thymus / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Exertier, C. / Reiser, J.-B. / Lantez, V. / Chouquet, A. / Bonneville, M. / Saulquin, X. / Housset, D. | ||||||
![]() | ![]() タイトル: human 199.16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2 著者: Exertier, C. / Reiser, J.-B. / Housset, D. | ||||||
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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ダウンロード
PDBx/mmCIF形式 | ![]() | 182.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 141.4 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 | ![]() | 465.4 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 475.2 KB | 表示 | |
XML形式データ | ![]() | 28.6 KB | 表示 | |
CIF形式データ | ![]() | 39.5 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 | ![]() 5nhtS S: 精密化の開始モデル |
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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 HL
#1: タンパク質 | 分子量: 31979.367 Da / 分子数: 1 / 変異: A245V / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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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) ![]() ![]() ![]() |
-T-cell receptor ... , 2種, 2分子 AB
#4: タンパク質 | 分子量: 23090.320 Da / 分子数: 1 / 変異: T158C,T158C,T158C / 由来タイプ: 組換発現 詳細: NUMBERING: RESIDUE 1 MATCH FIRST RESIDUE OF TRAV 12-2 DEFINED IN IMGT. ADDITIONAL SEQUENCE IN C-TER (ENDGGGCK) TO ENHANCE ALPHA-BETA CHAIN PAIRING. 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: A0A075B6T6, UniProt: A0A075B6X0, UniProt: A0A1B0GUM0, UniProt: P01848*PLUS |
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#5: タンパク質 | 分子量: 28292.430 Da / 分子数: 1 / 変異: S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C / 由来タイプ: 組換発現 詳細: NUMBERING: RESIDUE 1 MATCH FIRST RESIDUE OF TRBV 19 DEFINED IN IMGT. ADDITIONAL SEQUENCE IN C-TER (DQDRGGGCD) TO ENHANCE ALPHA-BETA CHAIN PAIRING. 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: A0A5B3, UniProt: A0A0C4ZKA8, UniProt: A0A075B6N1*PLUS |
-タンパク質・ペプチド / 非ポリマー , 2種, 2分子 P

#3: タンパク質・ペプチド | 分子量: 985.176 Da / 分子数: 1 / 変異: A27L / 由来タイプ: 合成 / 由来: (合成) ![]() |
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#6: 化合物 | ChemComp-NA / |
-詳細
Has protein modification | Y |
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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: 2.76 Å3/Da / 溶媒含有率: 55.42 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: PEG3350 11%, bis-tris propane pH 6.5 0.1M, KNa tartrate 0.1M |
-データ収集
回折 | 平均測定温度: 110 K |
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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: 2014年4月12日 |
放射 | モノクロメーター: mirror / 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: 0.97625 Å / 相対比: 1 |
反射 | 解像度: 3.25→48.53 Å / Num. obs: 16830 / % possible obs: 98.8 % / 冗長度: 3.3 % / CC1/2: 0.99 / Rsym value: 0.173 / Net I/σ(I): 6.28 |
反射 シェル | 解像度: 3.25→3.33 Å / 冗長度: 3.43 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1236 / CC1/2: 0.523 / Rsym value: 1.611 / % possible all: 98.7 |
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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: 5NHT 解像度: 3.25→48.53 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.837 / SU B: 50.604 / SU ML: 0.742 / 交差検証法: THROUGHOUT / ESU R Free: 0.759 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 109.51 Å2
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精密化ステップ | サイクル: 1 / 解像度: 3.25→48.53 Å
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拘束条件 |
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