+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6wol | ||||||
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タイトル | Next generation monomeric IgG4 Fc bound to neonatal Fc receptor | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / antibody constant region / fragment crystallizable (フラグメント結晶化可能領域) / mutated (突然変異) / neonatal Fc receptor | ||||||
機能・相同性 | 機能・相同性情報 IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / beta-2-microglobulin binding ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / beta-2-microglobulin binding / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / 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 binding / Regulation of Complement cascade / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / 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 / Regulation of actin dynamics for phagocytic cup formation / 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 / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / 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 / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / antibacterial humoral response / protein homotetramerization / Interleukin-4 and Interleukin-13 signaling / intracellular iron ion homeostasis / 獲得免疫系 / amyloid fibril formation / blood microparticle / learning or memory / endosome membrane / 免疫応答 / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / 小胞体 / ゴルジ体 / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / ゴルジ体 / 小胞体 / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / 生体膜 / identical protein binding / 細胞膜 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: 2.49 Å | ||||||
データ登録者 | Oganesyan, V.Y. / Shan, L. / van Dyk, N. / Dall'Acqua, W.F. | ||||||
引用 | ジャーナル: Commun Biol / 年: 2021 タイトル: In vivo pharmacokinetic enhancement of monomeric Fc and monovalent bispecific designs through structural guidance. 著者: Shan, L. / Dyk, N.V. / Haskins, N. / Cook, K.M. / Rosenthal, K.L. / Mazor, R. / Dragulin-Otto, S. / Jiang, Y. / Wu, H. / Dall'Acqua, W.F. / Borrok, M.J. / Damschroder, M.M. / Oganesyan, V. | ||||||
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 | 6wol.cif.gz | 134.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6wol.ent.gz | 101.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6wol.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/wo/6wol ftp://data.pdbj.org/pub/pdb/validation_reports/wo/6wol | 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
#1: タンパク質 | 分子量: 23753.797 Da / 分子数: 1 / 断片: domains Ch3 and Ch4 変異: L351F, S354E, T366R, P395K, F405R, Y407E, L432C, H433S, N434Y, Y436L, T437C, Q438 deleted 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IGHG4 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P01861 |
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#2: タンパク質 | 分子量: 29720.383 Da / 分子数: 1 / 断片: extracellular domain / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FCGRT, FCRN / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P55899 |
#3: タンパク質 | 分子量: 11748.160 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: Homo sapiens (ヒト) / 参照: UniProt: P61769 |
#4: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose |
#5: 水 | ChemComp-HOH / |
研究の焦点であるリガンドがあるか | N |
-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: 2.86 Å3/Da / 溶媒含有率: 57.04 % |
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法 / pH: 6 詳細: 0.2 M magnesium chloride hexahydrate, 1 M sodium iodide, 0.1 M MES, pH 6 and 20% PEG 6000 at a protein concentration of 6.35 mg/mL |
-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: SSRL / ビームライン: BL9-2 / 波長: 0.97946 Å |
検出器 | タイプ: DECTRIS PILATUS 300K / 検出器: PIXEL / 日付: 2018年6月22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: 0.97946 Å / 相対比: 1 |
反射 | 解像度: 2.49→36.1 Å / Num. obs: 26347 / % possible obs: 99.3 % / 冗長度: 6.4 % / Biso Wilson estimate: 45 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.086 / Net I/σ(I): 4.9 |
反射 シェル | 解像度: 2.49→2.6 Å / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2798 / CC1/2: 0.757 / Rpim(I) all: 0.374 |
-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: 5hvw 解像度: 2.49→36.1 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.882 / SU B: 11.398 / SU ML: 0.244 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.508 / ESU R Free: 0.295 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 123.71 Å2 / Biso mean: 45.346 Å2 / Biso min: 6.74 Å2
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精密化ステップ | サイクル: final / 解像度: 2.49→36.1 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.494→2.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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