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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: 4uq2 | |||||||||
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タイトル | Crystal structure of HLA-A1101 in complex with an azobenzene- containing peptide | |||||||||
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![]() | IMMUNE SYSTEM / AZOBENZENE / HLA-A / SYNTHETIC PEPTIDE | |||||||||
機能・相同性 | ![]() 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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / 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 / peptide antigen assembly with MHC class II protein complex / 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 iron ion transport / regulation of erythrocyte differentiation / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / MHC class I protein complex / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / positive regulation of protein binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus 類似検索 - 分子機能 | |||||||||
生物種 | ![]() SYNTHETIC CONSTRUCT (人工物) | |||||||||
手法 | ![]() ![]() | |||||||||
![]() | Thong, S.Y. / Yap, J.W. / Lim, P.Y. / Verhelst, S.H. / Lescar, J. / Meijers, R. / Grotenbreg, G.M. | |||||||||
![]() | ![]() タイトル: Bioorthogonal Cleavage and Exchange of Major Histocompatibility Complex Ligands by Employing Azobenzene-Containing Peptides. 著者: Choo, J.A.L. / Thong, S.Y. / Yap, J. / Van Esch, W.J.E. / Raida, M. / Meijers, R. / Lescar, J. / Verhelst, S.H.L. / Grotenbreg, G.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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ダウンロード
PDBx/mmCIF形式 | ![]() | 176.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 143 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 | ![]() | 464.1 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 475.8 KB | 表示 | |
XML形式データ | ![]() | 31.6 KB | 表示 | |
CIF形式データ | ![]() | 45.3 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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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非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域: Component-ID: 1 / Refine code: 4
NCSアンサンブル:
NCS oper:
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要素
#1: タンパク質 | 分子量: 31855.051 Da / 分子数: 2 / 断片: EXTRACELLULAR DOMAIN, RESIDUES 25-299 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 11748.160 Da / 分子数: 2 / 断片: RESIDUES 21-119 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #3: タンパク質・ペプチド | 分子量: 990.198 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) SYNTHETIC CONSTRUCT (人工物) #4: 水 | ChemComp-HOH / | 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: 2.82 Å3/Da / 溶媒含有率: 56.42 % / 解説: NONE |
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結晶化 | 詳細: 0.2 M AMMONIUM SULFATE, 15% W/V PEG4000, 0.1M TRI-SODIUM CITRATE PH5.6 |
-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: RIGAKU R-AXIS IV++ / 検出器: IMAGE PLATE / 日付: 2012年9月19日 / 詳細: MIRROR |
放射 | モノクロメーター: CU / 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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2.43→29.93 Å / Num. obs: 35112 / % possible obs: 94.7 % / Observed criterion σ(I): 3 / 冗長度: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.4 |
反射 シェル | 解像度: 2.43→2.56 Å / 冗長度: 4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 6.8 / % possible all: 90.7 |
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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: PDB ENTRY 2HN7 解像度: 2.43→29.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.72 / SU ML: 0.198 / 交差検証法: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.285 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 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 / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 30.344 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.43→29.93 Å
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拘束条件 |
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