+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7s8e | ||||||
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タイトル | STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PHOSPHOPEPTIDE AND BOUND GLYCEROL | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / HLA / MLL PEPTIDE / MHC-I (MHCクラスI分子) / HLA-B*07:02 / HLA-B7 / IMMUNITY / PHOSPHOPEPTIDE / NEOANTIGEN (抗原) / CANCER (悪性腫瘍) | ||||||
機能・相同性 | 機能・相同性情報 protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / regulation of short-term neuronal synaptic plasticity / regulation of interleukin-12 production / regulation of dendritic cell differentiation ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / regulation of short-term neuronal synaptic plasticity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / T-helper 2 cell differentiation / definitive hemopoiesis / histone H3K4 methyltransferase activity / regulation of T cell anergy / regulation of interleukin-6 production / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / 脱分極 / MLL1 complex / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / transcription initiation-coupled chromatin remodeling / spleen development / cellular response to transforming growth factor beta stimulus / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / 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 / post-embryonic development / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / circadian regulation of gene expression / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / negative regulation of forebrain neuron differentiation / visual learning / protein modification process / 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 / PKMTs methylate histone lysines / positive regulation of T cell cytokine production / defense response / 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 / Transcriptional regulation of granulopoiesis / 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 / 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 / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.6 Å | ||||||
データ登録者 | Patskovsky, Y. / Nyovanie, S. / Patskovska, L. / Natarajan, A. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. ...Patskovsky, Y. / Nyovanie, S. / Patskovska, L. / Natarajan, A. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R. / Findeis, M. / Hurwitz, A. / Van Dijk, M. / Buell, J. / Underwood, D. / Krogsgaard, M. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Molecular mechanism of phosphopeptide neoantigen immunogenicity. 著者: Patskovsky, Y. / Natarajan, A. / Patskovska, L. / Nyovanie, S. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R.B. / Findeis, M.A. ...著者: Patskovsky, Y. / Natarajan, A. / Patskovska, L. / Nyovanie, S. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R.B. / Findeis, M.A. / Hurwitz, A. / Van Dijk, M. / Chantzoura, E. / Yague, A.S. / Pollack Smith, D. / Buell, J.S. / Underwood, D. / Krogsgaard, M. | ||||||
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 | 7s8e.cif.gz | 111.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7s8e.ent.gz | 82.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7s8e.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/s8/7s8e ftp://data.pdbj.org/pub/pdb/validation_reports/s8/7s8e | HTTPS FTP |
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-関連構造データ
関連構造データ | 7rzdC 7rzjSC 7s79C 7s7dC 7s7eC 7s7fC 7s8aC 7s8fC 7s8iC 7s8jC S: 精密化の開始モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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
#1: タンパク質 | 分子量: 31962.016 Da / 分子数: 1 / 断片: UNP RESIDUES 25-299 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-B, HLAB / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P01889 | ||||
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#2: タンパク質 | 分子量: 11879.356 Da / 分子数: 1 / 断片: UNP residues 21-119 / 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 / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P61769 | ||||
#3: タンパク質・ペプチド | 分子量: 1109.108 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q03164 | ||||
#4: 化合物 | ChemComp-GOL / #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
-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: 2.89 Å3/Da / 溶媒含有率: 57.53 % / 解説: RODS |
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結晶化 | 温度: 290 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8 詳細: 18-24%PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE |
-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: APS / ビームライン: 19-BM / 波長: 0.9794 Å |
検出器 | タイプ: ADSC QUANTUM 210r / 検出器: CCD / 日付: 2018年11月13日 / 詳細: SI 111 CRYSTAL |
放射 | モノクロメーター: SI 111 CRYSTAL / 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: 0.9794 Å / 相対比: 1 |
反射 | 解像度: 1.6→45.54 Å / Num. obs: 69841 / % possible obs: 100 % / 冗長度: 6.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.3 |
反射 シェル | 解像度: 1.6→1.63 Å / 冗長度: 6.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3393 / CC1/2: 0.55 / % possible all: 100 |
-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: 7RZJ 解像度: 1.6→45.54 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.652 / SU ML: 0.056 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075 / 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: 1.3 Å / 溶媒モデル: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 104.38 Å2 / Biso mean: 24.974 Å2 / Biso min: 11.16 Å2
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精密化ステップ | サイクル: final / 解像度: 1.6→45.54 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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