+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8esv | |||||||||
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タイトル | Structure of human ADAM10-Tspan15 complex bound to 11G2 vFab | |||||||||
要素 |
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キーワード | MEMBRANE PROTEIN (膜タンパク質) / Protease (プロテアーゼ) / Metalloprotease (金属プロテアーゼ) / Tetraspanin (テトラスパニン) / Sheddase / Adhesion (接着) | |||||||||
機能・相同性 | 機能・相同性情報 regulation of membrane protein ectodomain proteolysis / ADAM10 endopeptidase / constitutive protein ectodomain proteolysis / regulation of vasculature development / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / protein catabolic process at postsynapse / postsynapse organization / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant ...regulation of membrane protein ectodomain proteolysis / ADAM10 endopeptidase / constitutive protein ectodomain proteolysis / regulation of vasculature development / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / protein catabolic process at postsynapse / postsynapse organization / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / : / regulation of Notch signaling pathway / perinuclear endoplasmic reticulum / positive regulation of T cell chemotaxis / pore complex assembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / tetraspanin-enriched microdomain / metallodipeptidase activity / negative regulation of cell adhesion / adherens junction organization / regulation of postsynapse organization / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / クラスリン / Golgi-associated vesicle / Signaling by EGFR / cochlea development / negative regulation of Notch signaling pathway / pore complex / amyloid precursor protein catabolic process / tertiary granule membrane / membrane protein ectodomain proteolysis / protein maturation / Collagen degradation / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / response to tumor necrosis factor / specific granule membrane / Notchシグナリング / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Degradation of the extracellular matrix / Activated NOTCH1 Transmits Signal to the Nucleus / synaptic membrane / NOTCH3 Activation and Transmission of Signal to the Nucleus / integrin-mediated signaling pathway / protein localization to plasma membrane / Post-translational protein phosphorylation / 接着結合 / protein processing / metalloendopeptidase activity / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SH3 domain binding / metallopeptidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / integrin binding / cell-cell signaling / 細胞結合 / late endosome membrane / positive regulation of cell growth / endopeptidase activity / in utero embryonic development / postsynaptic density / molecular adaptor activity / nuclear body / positive regulation of cell migration / Amyloid fiber formation / 神経繊維 / 小胞体 / ゴルジ体 / protein phosphorylation / negative regulation of gene expression / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / 樹状突起 / glutamatergic synapse / positive regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / ゴルジ体 / enzyme binding / 細胞膜 / protein homodimerization activity / extracellular exosome / 生体膜 / metal ion binding / 細胞核 / 細胞膜 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) Mus musculus (ハツカネズミ) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.3 Å | |||||||||
データ登録者 | Lipper, C.H. / Blacklow, S.C. | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Cell / 年: 2023 タイトル: Structural basis for membrane-proximal proteolysis of substrates by ADAM10. 著者: Colin H Lipper / Emily D Egan / Khal-Hentz Gabriel / Stephen C Blacklow / 要旨: The endopeptidase ADAM10 is a critical catalyst for the regulated proteolysis of key drivers of mammalian development, physiology, and non-amyloidogenic cleavage of APP as the primary α-secretase. ...The endopeptidase ADAM10 is a critical catalyst for the regulated proteolysis of key drivers of mammalian development, physiology, and non-amyloidogenic cleavage of APP as the primary α-secretase. ADAM10 function requires the formation of a complex with a C8-tetraspanin protein, but how tetraspanin binding enables positioning of the enzyme active site for membrane-proximal cleavage remains unknown. We present here a cryo-EM structure of a vFab-ADAM10-Tspan15 complex, which shows that Tspan15 binding relieves ADAM10 autoinhibition and acts as a molecular measuring stick to position the enzyme active site about 20 Å from the plasma membrane for membrane-proximal substrate cleavage. Cell-based assays of N-cadherin shedding establish that the positioning of the active site by the interface between the ADAM10 catalytic domain and the bound tetraspanin influences selection of the preferred cleavage site. Together, these studies reveal the molecular mechanism underlying ADAM10 proteolysis at membrane-proximal sites and offer a roadmap for its modulation in disease. | |||||||||
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 | 8esv.cif.gz | 206.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8esv.ent.gz | 153.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8esv.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/es/8esv ftp://data.pdbj.org/pub/pdb/validation_reports/es/8esv | HTTPS FTP |
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-関連構造データ
関連構造データ | 28580MC M: このデータのモデリングに利用したマップデータ 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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-要素
-タンパク質 , 2種, 2分子 AB
#1: タンパク質 | 分子量: 60477.340 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: ADAM10, KUZ, MADM / プラスミド: pRK5M / 細胞株 (発現宿主): Expi293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O14672, ADAM10 endopeptidase |
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#2: タンパク質 | 分子量: 34740.469 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: TSPAN15, NET7, TM4SF15, UNQ677/PRO1311 / プラスミド: pcDNA3.1/Hygro(+) / 細胞株 (発現宿主): Expi293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O95858 |
-抗体 , 2種, 2分子 HL
#3: 抗体 | 分子量: 24135.105 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / プラスミド: pFUSE-hIgG1-Fc2 詳細 (発現宿主): Heavy and light chain in same vector with P2A sequence 細胞株 (発現宿主): Expi293F / 発現宿主: Homo sapiens (ヒト) |
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#4: 抗体 | 分子量: 24185.803 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / プラスミド: pFUSE-hIgG1-Fc2 詳細 (発現宿主): Heavy and light chain in same vector with P2A sequence 細胞株 (発現宿主): Expi293F / 発現宿主: Homo sapiens (ヒト) |
-糖 , 3種, 3分子
#5: 多糖 | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#6: 多糖 | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#7: 糖 | ChemComp-NAG / |
-非ポリマー , 4種, 5分子
#8: 化合物 | ChemComp-CA / |
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#9: 化合物 | ChemComp-ZN / |
#10: 化合物 | ChemComp-BAT / |
#11: 化合物 |
-詳細
研究の焦点であるリガンドがあるか | N |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 |
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分子量 | 実験値: NO | |||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.4 | |||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 2.1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: This sample was monodisperse | |||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Quantifoil | |||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 295 K / 詳細: Blot for 7 seconds with a blot force of 15 |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 105000 X / 最大 デフォーカス(公称値): 2200 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm |
試料ホルダ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 1.3 sec. / 電子線照射量: 51.99 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 10037 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 178031 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 空間: REAL |