+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7tvd | ||||||
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タイトル | Crystal structure of the kinase domain of EGFR exon-19 (del-747-749) mutant | ||||||
要素 | Epidermal growth factor receptor | ||||||
キーワード | TRANSFERASE / EGFR / exon-19 / kinase / ONCOPROTEIN | ||||||
機能・相同性 | 機能・相同性情報 response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity ...response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / response to UV-A / epidermal growth factor binding / PLCG1 events in ERBB2 signaling / tongue development / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Signaling by EGFR / response to cobalamin / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / eyelid development in camera-type eye / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / embryonic placenta development / positive regulation of bone resorption / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / cellular response to cadmium ion / positive regulation of DNA repair / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / positive regulation of synaptic transmission, glutamatergic / cellular response to dexamethasone stimulus / ossification / neurogenesis / regulation of ERK1 and ERK2 cascade / basal plasma membrane / neuron projection morphogenesis / positive regulation of superoxide anion generation / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / cellular response to estradiol stimulus / positive regulation of epithelial cell proliferation / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / liver regeneration / positive regulation of protein localization to plasma membrane / EGFR downregulation / cellular response to amino acid stimulus / positive regulation of smooth muscle cell proliferation / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / lung development / clathrin-coated endocytic vesicle membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / negative regulation of protein catabolic process / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / kinase binding / ruffle membrane / positive regulation of miRNA transcription / cell-cell adhesion 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: 2.96 Å | ||||||
データ登録者 | Ashtekar, K.D. / Stayrook, S.E. / Lemmon, M.A. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2022 タイトル: Biochemical and structural basis for differential inhibitor sensitivity of EGFR with distinct exon 19 mutations. 著者: van Alderwerelt van Rosenburgh, I.K. / Lu, D.M. / Grant, M.J. / Stayrook, S.E. / Phadke, M. / Walther, Z. / Goldberg, S.B. / Politi, K. / Lemmon, M.A. / Ashtekar, K.D. / Tsutsui, Y. | ||||||
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 | 7tvd.cif.gz | 157.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7tvd.ent.gz | 104.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7tvd.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 | 7tvd_validation.pdf.gz | 425.7 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7tvd_full_validation.pdf.gz | 432.2 KB | 表示 | |
XML形式データ | 7tvd_validation.xml.gz | 12.7 KB | 表示 | |
CIF形式データ | 7tvd_validation.cif.gz | 16 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/tv/7tvd ftp://data.pdbj.org/pub/pdb/validation_reports/tv/7tvd | HTTPS FTP |
-関連構造データ
関連構造データ | 1m17S S: 精密化の開始モデル |
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類似構造データ |
-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: 38237.191 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: EGFR, ERBB, ERBB1, HER1 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P00533, receptor protein-tyrosine kinase |
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-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: 3.64 Å3/Da / 溶媒含有率: 66.16 % |
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結晶化 | 温度: 289.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: 28% PEG 400, 0.1 M Na Hepes pH 7.5, 0.2 M Calcium Chloride |
-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: 24-ID-C / 波長: 0.97918 Å | |||||||||||||||||||||||||||
検出器 | タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年3月19日 / 詳細: undulator | |||||||||||||||||||||||||||
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: 0.97918 Å / 相対比: 1 | |||||||||||||||||||||||||||
反射 | 解像度: 2.96→105.66 Å / Num. obs: 11749 / % possible obs: 100 % / 冗長度: 36.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.044 / Rrim(I) all: 0.263 / Net I/σ(I): 15.4 / Num. measured all: 423785 | |||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1 / % possible all: 100
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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: 分子置換 開始モデル: 1M17 解像度: 2.96→74.71 Å / SU ML: 0.4085 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 35.9126 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 104.92 Å2 | ||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.96→74.71 Å
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拘束条件 |
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LS精密化 シェル |
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精密化 TLS | 手法: refined / Origin x: -60.3983808351 Å / Origin y: 7.60852047851 Å / Origin z: 25.513823797 Å
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精密化 TLSグループ | Selection details: all |