+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5j11 | ||||||
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タイトル | Structure of human TSLP in complex with TSLPR and IL-7Ralpha | ||||||
要素 |
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キーワード | SIGNALING PROTEIN / cytokine inflammation TSLP signaling complex | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of chemokine (C-C motif) ligand 1 production / positive regulation of granulocyte colony-stimulating factor production / interleukin-7 receptor activity / interleukin-7 receptor binding / interleukin-7-mediated signaling pathway / positive regulation of mast cell activation / negative regulation of T cell mediated cytotoxicity / positive regulation of receptor signaling pathway via STAT / regulation of DNA recombination / positive regulation of cytokine-mediated signaling pathway ...positive regulation of chemokine (C-C motif) ligand 1 production / positive regulation of granulocyte colony-stimulating factor production / interleukin-7 receptor activity / interleukin-7 receptor binding / interleukin-7-mediated signaling pathway / positive regulation of mast cell activation / negative regulation of T cell mediated cytotoxicity / positive regulation of receptor signaling pathway via STAT / regulation of DNA recombination / positive regulation of cytokine-mediated signaling pathway / positive regulation of T cell differentiation in thymus / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / negative regulation of T cell apoptotic process / cellular homeostasis / cytokine receptor activity / regulation of cell size / B cell proliferation / cytokine binding / T cell homeostasis / hemopoiesis / cell surface receptor signaling pathway via JAK-STAT / B cell homeostasis / positive regulation of interleukin-10 production / defense response to fungus / lymph node development / coreceptor activity / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of chemokine production / Interleukin-7 signaling / antigen binding / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / clathrin-coated endocytic vesicle membrane / cell morphogenesis / T cell mediated cytotoxicity / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / positive regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / gene expression / T cell differentiation in thymus / defense response to Gram-negative bacterium / receptor complex / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / signal transduction / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytosol 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: 2.56 Å | ||||||
データ登録者 | Verstraete, K. / Savvides, S.N. | ||||||
引用 | ジャーナル: Nat Commun / 年: 2017 タイトル: Structure and antagonism of the receptor complex mediated by human TSLP in allergy and asthma. 著者: Kenneth Verstraete / Frank Peelman / Harald Braun / Juan Lopez / Dries Van Rompaey / Ann Dansercoer / Isabel Vandenberghe / Kris Pauwels / Jan Tavernier / Bart N Lambrecht / Hamida Hammad / ...著者: Kenneth Verstraete / Frank Peelman / Harald Braun / Juan Lopez / Dries Van Rompaey / Ann Dansercoer / Isabel Vandenberghe / Kris Pauwels / Jan Tavernier / Bart N Lambrecht / Hamida Hammad / Hans De Winter / Rudi Beyaert / Guy Lippens / Savvas N Savvides / 要旨: The pro-inflammatory cytokine thymic stromal lymphopoietin (TSLP) is pivotal to the pathophysiology of widespread allergic diseases mediated by type 2 helper T cell (Th2) responses, including asthma ...The pro-inflammatory cytokine thymic stromal lymphopoietin (TSLP) is pivotal to the pathophysiology of widespread allergic diseases mediated by type 2 helper T cell (Th2) responses, including asthma and atopic dermatitis. The emergence of human TSLP as a clinical target against asthma calls for maximally harnessing its therapeutic potential via structural and mechanistic considerations. Here we employ an integrative experimental approach focusing on productive and antagonized TSLP complexes and free cytokine. We reveal how cognate receptor TSLPR allosterically activates TSLP to potentiate the recruitment of the shared interleukin 7 receptor α-chain (IL-7Rα) by leveraging the flexibility, conformational heterogeneity and electrostatics of the cytokine. We further show that the monoclonal antibody Tezepelumab partly exploits these principles to neutralize TSLP activity. Finally, we introduce a fusion protein comprising a tandem of the TSLPR and IL-7Rα extracellular domains, which harnesses the mechanistic intricacies of the TSLP-driven receptor complex to manifest high antagonistic potency. | ||||||
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 | 5j11.cif.gz | 398.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5j11.ent.gz | 331.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5j11.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
文書・要旨 | 5j11_validation.pdf.gz | 479.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5j11_full_validation.pdf.gz | 483.3 KB | 表示 | |
XML形式データ | 5j11_validation.xml.gz | 19.3 KB | 表示 | |
CIF形式データ | 5j11_validation.cif.gz | 26.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j1/5j11 ftp://data.pdbj.org/pub/pdb/validation_reports/j1/5j11 | HTTPS FTP |
-関連構造データ
-リンク
-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 , 3種, 3分子 ABC
#1: タンパク質 | 分子量: 16523.906 Da / 分子数: 1 変異: Residues 127 to 131 were deleted in the construct used for crystallisation. 由来タイプ: 組換発現 詳細: Before crystallisation, the N-terminal His-tag (residues 1 - 17, MGSSHHHHHHSSGLVPR) was removed by thrombin cleavage. Residues 127 to 131 of TSLP (127-RRKRK-131) (according to the reference ...詳細: Before crystallisation, the N-terminal His-tag (residues 1 - 17, MGSSHHHHHHSSGLVPR) was removed by thrombin cleavage. Residues 127 to 131 of TSLP (127-RRKRK-131) (according to the reference sequence numbering scheme for TSLP) were deleted in the construct used for crystallization. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TSLP / プラスミド: pET15b-hTSLPdelta127-131 詳細 (発現宿主): ORF cloned between NdeI and BamHI sites 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q969D9 |
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#2: タンパク質 | 分子量: 27592.170 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: Before crystallisation, the N-terminal His-tag (residues 1 - 17, MGSSHHHHHHSSGLVPR) was removed by thrombin cleavage. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IL7R / プラスミド: pET15b-hIL7Ralpha 詳細 (発現宿主): ORF cloned between NdeI and BamHI sites 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: D6RGV2, UniProt: P16871*PLUS |
#3: タンパク質 | 分子量: 26573.562 Da / 分子数: 1 / 変異: N47Q / 由来タイプ: 組換発現 詳細: The signal peptide (residues 1 - 24) is removed from the mature protein. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CRLF2, CRL2, ILXR, TSLPR / プラスミド: pcDNA4/TO-hTSLPR-N47Q-His 詳細 (発現宿主): stable cell line, tetracycline inducible expression 細胞株 (発現宿主): HEK293S MGAT1-/- / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9HC73 |
-糖 , 1種, 2分子
#5: 糖 |
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-非ポリマー , 2種, 30分子
#4: 化合物 | ChemComp-PGE / |
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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: 3.05 Å3/Da / 溶媒含有率: 59.72 % |
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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 / pH: 8.8 詳細: 0.02 M Citric acid 0.08 M BIS-TRIS propane 16% w/v polyethylene glycol 3350 |
-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: シンクロトロン / サイト: SOLEIL / ビームライン: PROXIMA 2 / 波長: 0.9801 Å |
検出器 | タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2015年1月30日 |
放射 | モノクロメーター: Si[111] / 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: 0.9801 Å / 相対比: 1 |
反射 | 解像度: 2.56→50 Å / Num. obs: 24638 / % possible obs: 97.8 % / 冗長度: 3.2 % / Biso Wilson estimate: 69.9 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.062 / Net I/σ(I): 14.2 |
反射 シェル | 解像度: 2.56→2.72 Å / 冗長度: 3.1 % / Mean I/σ(I) obs: 1.7 / Rrim(I) all: 0.776 / % possible all: 94.2 |
-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: X-ray structure of human TSLP in complex with human TSLPR and mouse IL-7Ralpha; PDB 3DI2: chain B 解像度: 2.56→45.76 Å / Cor.coef. Fo:Fc: 0.9349 / Cor.coef. Fo:Fc free: 0.9285 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.319 / SU Rfree Blow DPI: 0.219
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原子変位パラメータ | Biso mean: 88.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0.328 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.56→45.76 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.56→2.67 Å / Total num. of bins used: 12
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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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