+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7lfr | ||||||
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タイトル | Crystal structure of the epidermal growth factor receptor extracellular region with R84K mutation in complex with epiregulin crystallized with spermine | ||||||
要素 |
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キーワード | SIGNALING PROTEIN / receptor / epiregulin / glioblastoma / cancer / mutation / extracellular / asymmetric / dimer / ErbB1 / EGFR | ||||||
機能・相同性 | 機能・相同性情報 luteinizing hormone signaling pathway / ovarian cumulus expansion / ovulation / ERBB4-ERBB4 signaling pathway / negative regulation of smooth muscle cell differentiation / ERBB2-ERBB4 signaling pathway / primary follicle stage / female meiotic nuclear division / PI3K events in ERBB4 signaling / positive regulation of innate immune response ...luteinizing hormone signaling pathway / ovarian cumulus expansion / ovulation / ERBB4-ERBB4 signaling pathway / negative regulation of smooth muscle cell differentiation / ERBB2-ERBB4 signaling pathway / primary follicle stage / female meiotic nuclear division / PI3K events in ERBB4 signaling / positive regulation of innate immune response / 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 / oocyte maturation / diterpenoid metabolic process / mRNA transcription / 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 / epidermal growth factor receptor binding / 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 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / eyelid development in camera-type eye / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / positive regulation of cell division / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / keratinocyte proliferation / negative regulation of mitotic cell cycle / hair follicle development / SHC1 events in ERBB4 signaling / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / MAP kinase kinase kinase activity / positive regulation of protein kinase activity / embryonic placenta development / anatomical structure morphogenesis / positive regulation of bone resorption / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / Nuclear signaling by ERBB4 / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / keratinocyte differentiation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / cellular response to cadmium ion / positive regulation of DNA repair / EGFR Transactivation by Gastrin / 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 mitotic nuclear division / positive regulation of synaptic transmission, glutamatergic / ossification / cellular response to dexamethasone stimulus / basal plasma membrane / neurogenesis / regulation of ERK1 and ERK2 cascade / neuron projection morphogenesis / positive regulation of superoxide anion generation / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / positive regulation of cytokine production / cellular response to estradiol stimulus / NOTCH3 Activation and Transmission of Signal to the Nucleus 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: 3.2 Å | ||||||
データ登録者 | Hu, C. / Leche II, C.A. / Stayrook, S.E. / Ferguson, K.M. / Lemmon, M.A. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nature / 年: 2022 タイトル: Glioblastoma mutations alter EGFR dimer structure to prevent ligand bias. 著者: Hu, C. / Leche 2nd, C.A. / Kiyatkin, A. / Yu, Z. / Stayrook, S.E. / Ferguson, K.M. / Lemmon, M.A. | ||||||
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 | 7lfr.cif.gz | 223.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7lfr.ent.gz | 176.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7lfr.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 | 7lfr_validation.pdf.gz | 797.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7lfr_full_validation.pdf.gz | 817.5 KB | 表示 | |
XML形式データ | 7lfr_validation.xml.gz | 40.8 KB | 表示 | |
CIF形式データ | 7lfr_validation.cif.gz | 54 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/lf/7lfr ftp://data.pdbj.org/pub/pdb/validation_reports/lf/7lfr | 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 / タンパク質・ペプチド , 2種, 4分子 ABCD
#1: タンパク質 | 分子量: 55803.461 Da / 分子数: 2 / 変異: R84K / 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 #2: タンパク質・ペプチド | 分子量: 5480.307 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EREG 発現宿主: Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: O14944 |
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-糖 , 4種, 9分子
#3: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||||
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#4: 糖 | ChemComp-NAG / #5: 糖 | #6: 糖 | ChemComp-BMA / | |
-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: 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: 2.64 Å3/Da / 溶媒含有率: 53 % |
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結晶化 | 温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: 8 mg/ml protein, 100 mM HEPES (pH 7.5), 12% PEG3350, 10 mM spermine tetrahydrochloride |
-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: 23-ID-B / 波長: 1.0332 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年2月14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: 1.0332 Å / 相対比: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 3.2→99.006 Å / Num. obs: 22984 / % possible obs: 99.8 % / 冗長度: 8.4 % / Rpim(I) all: 0.073 / Rrim(I) all: 0.215 / Rsym value: 0.202 / Net I/av σ(I): 3.1 / Net I/σ(I): 9 / Num. measured all: 193914 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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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: 5WB7 解像度: 3.2→43.6 Å / SU ML: 0.47 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 30.43 / 立体化学のターゲット値: ML
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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 max: 170.45 Å2 / Biso mean: 92.041 Å2 / Biso min: 40.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 3.2→43.6 Å
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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