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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: 5i04 | ||||||||||||||||||||||||
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タイトル | Crystal structure of the orphan region of human endoglin/CD105 | ||||||||||||||||||||||||
![]() | Maltose-binding periplasmic protein,Endoglin | ||||||||||||||||||||||||
![]() | SIGNALING PROTEIN / ORPHAN DOMAIN / ANGIOGENESIS / GLYCOPROTEIN / RECEPTOR | ||||||||||||||||||||||||
機能・相同性 | ![]() extracellular matrix constituent secretion / atrial cardiac muscle tissue morphogenesis / detection of hypoxia / atrioventricular canal morphogenesis / vascular associated smooth muscle cell development / endothelial microparticle / venous blood vessel morphogenesis / dorsal aorta morphogenesis / negative regulation of nitric-oxide synthase activity / positive regulation of vascular associated smooth muscle cell differentiation ...extracellular matrix constituent secretion / atrial cardiac muscle tissue morphogenesis / detection of hypoxia / atrioventricular canal morphogenesis / vascular associated smooth muscle cell development / endothelial microparticle / venous blood vessel morphogenesis / dorsal aorta morphogenesis / negative regulation of nitric-oxide synthase activity / positive regulation of vascular associated smooth muscle cell differentiation / cell migration involved in endocardial cushion formation / central nervous system vasculogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / transforming growth factor beta receptor activity / regulation of transforming growth factor beta receptor signaling pathway / galactose binding / positive regulation of systemic arterial blood pressure / cardiac atrium morphogenesis / smooth muscle tissue development / type II transforming growth factor beta receptor binding / activin binding / type I transforming growth factor beta receptor binding / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / regulation of phosphorylation / positive regulation of BMP signaling pathway / glycosaminoglycan binding / transforming growth factor beta binding / signaling receptor activator activity / artery morphogenesis / endocardial cushion morphogenesis / branching involved in blood vessel morphogenesis / detection of maltose stimulus / maltose transport complex / heart looping / negative regulation of endothelial cell proliferation / carbohydrate transport / positive regulation of SMAD protein signal transduction / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / positive regulation of collagen biosynthetic process / extracellular matrix disassembly / epithelial to mesenchymal transition / vasculogenesis / BMP signaling pathway / regulation of cell adhesion / coreceptor activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / transforming growth factor beta receptor signaling pathway / cell chemotaxis / negative regulation of cell migration / cell motility / negative regulation of transforming growth factor beta receptor signaling pathway / wound healing / bone development / cellular response to mechanical stimulus / positive regulation of angiogenesis / transmembrane signaling receptor activity / cell migration / outer membrane-bounded periplasmic space / regulation of cell population proliferation / periplasmic space / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / response to hypoxia / nuclear body / cell adhesion / response to xenobiotic stimulus / positive regulation of protein phosphorylation / external side of plasma membrane / negative regulation of gene expression / focal adhesion / DNA damage response / regulation of DNA-templated transcription / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | ||||||||||||||||||||||||
生物種 | ![]() ![]() ![]() | ||||||||||||||||||||||||
手法 | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Saito, T. / Bokhove, M. / de Sanctis, D. / Jovine, L. | ||||||||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural Basis of the Human Endoglin-BMP9 Interaction: Insights into BMP Signaling and HHT1. 著者: Saito, T. / Bokhove, M. / Croci, R. / Zamora-Caballero, S. / Han, L. / Letarte, M. / de Sanctis, D. / Jovine, L. #1: ジャーナル: J. Biol. Chem. / 年: 1990 タイトル: Primary structure of endoglin, an RGD-containing glycoprotein of human endothelial cells. 著者: Gougos, A. / Letarte, M. #2: ジャーナル: J. Biol. Chem. / 年: 2011 タイトル: Soluble endoglin specifically binds bone morphogenetic proteins 9 and 10 via its orphan domain, inhibits blood vessel formation, and suppresses tumor growth. 著者: Castonguay, R. / Werner, E.D. / Matthews, R.G. / Presman, E. / Mulivor, A.W. / Solban, N. / Sako, D. / Pearsall, R.S. / Underwood, K.W. / Seehra, J. / Kumar, R. / Grinberg, A.V. #3: ジャーナル: PLoS ONE / 年: 2012 タイトル: Structural and functional insights into endoglin ligand recognition and binding. 著者: Alt, A. / Miguel-Romero, L. / Donderis, J. / Aristorena, M. / Blanco, F.J. / Round, A. / Rubio, V. / Bernabeu, C. / Marina, A. #4: ジャーナル: PLoS ONE / 年: 2012 タイトル: Endoglin requirement for BMP9 signaling in endothelial cells reveals new mechanism of action for selective anti-endoglin antibodies. 著者: Nolan-Stevaux, O. / Zhong, W. / Culp, S. / Shaffer, K. / Hoover, J. / Wickramasinghe, D. / Ruefli-Brasse, A. | ||||||||||||||||||||||||
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 | ![]() | 275.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 221.1 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-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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要素
#1: タンパク質 | 分子量: 75254.336 Da / 分子数: 1 変異: I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, ...変異: I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N 由来タイプ: 組換発現 詳細: THIS PROTEIN IS A CHIMERA. RESIDUES 56-422 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I57T, D137A, ...詳細: THIS PROTEIN IS A CHIMERA. RESIDUES 56-422 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A AND R422N (CORRESPONDING TO I28T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 426-737 ARE FROM HUMAN ENDOGLIN PROTEIN AND CORRESPOND TO RESIDUES 26-337 OF SWISS-PROT DATABASE ENTRY P17813. SUBTRACTING 400 FROM THE PDB ENTRY RESIDUE NUMBERING RESULTS IN THE NUMBERING ACCORDING TO UNIPROT ENTRY P17813. 由来: (組換発現) ![]() ![]() ![]() Cell: Endothelial / 遺伝子: malE, b4034, JW3994, ENG, END / プラスミド: pHLsec / 細胞株 (発現宿主): HEK293S / 発現宿主: ![]() | ||
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#2: 多糖 | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | ||
#3: 糖 | ChemComp-NAG / | ||
#4: 化合物 | #5: 水 | ChemComp-HOH / | |
-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: 3.02 Å3/Da / 溶媒含有率: 57.8 % / 解説: Droplet |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5 / 詳細: 30% PEG 1000, 0.1 M TRIS-HCL / PH範囲: 7.0-8.5 |
-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: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年9月10日 |
放射 | モノクロメーター: Si Single 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: 0.97625 Å / 相対比: 1 |
反射 | 解像度: 2.42→45.74 Å / Num. obs: 33737 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / 冗長度: 3.4 % / Biso Wilson estimate: 70.03 Å2 / Rsym value: 0.046 / Net I/σ(I): 11.76 |
反射 シェル | 解像度: 2.42→2.49 Å / 冗長度: 3.5 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 1.25 / % possible all: 98.5 |
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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: 3SEX, 3SET, 4WRN 解像度: 2.42→45.737 Å / SU ML: 0.47 / 交差検証法: FREE R-VALUE / σ(F): 1.39 / 位相誤差: 35.15
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溶媒の処理 | 減衰半径: 0.6 Å / VDWプローブ半径: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 76.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.42→45.737 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION
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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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