+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1n8y | |||||||||
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タイトル | Crystal structure of the extracellular region of rat HER2 | |||||||||
要素 | protooncoprotein | |||||||||
キーワード | TRANSFERASE (転移酵素) / tyrosin kinase receptor / cell surface receptor (細胞表面受容体) | |||||||||
機能・相同性 | 機能・相同性情報 Signaling by ERBB2 / GRB7 events in ERBB2 signaling / ERBB2 Activates PTK6 Signaling / Drug-mediated inhibition of ERBB2 signaling / GRB2 events in ERBB2 signaling / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / Downregulation of ERBB2 signaling / Sema4D induced cell migration and growth-cone collapse ...Signaling by ERBB2 / GRB7 events in ERBB2 signaling / ERBB2 Activates PTK6 Signaling / Drug-mediated inhibition of ERBB2 signaling / GRB2 events in ERBB2 signaling / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / Downregulation of ERBB2 signaling / Sema4D induced cell migration and growth-cone collapse / SHC1 events in ERBB2 signaling / PIP3 activates AKT signaling / negative regulation of immature T cell proliferation in thymus / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / mammary gland involution / immature T cell proliferation in thymus / RNA polymerase I core binding / lateral loop / glial cell differentiation / semaphorin receptor complex / sympathetic nervous system development / peripheral nervous system development / regulation of microtubule-based process / ErbB-3 class receptor binding / motor neuron axon guidance / positive regulation of Ras protein signal transduction / RAF/MAP kinase cascade / neurotransmitter receptor localization to postsynaptic specialization membrane / tongue development / positive regulation of Rho protein signal transduction / ERBB2-EGFR signaling pathway / neuromuscular junction development / positive regulation of transcription by RNA polymerase I / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / regulation of cell differentiation / 微絨毛 / semaphorin-plexin signaling pathway / estrous cycle / positive regulation of protein targeting to membrane / positive regulation of cell adhesion / response to axon injury / coreceptor activity / Schwann cell development / skeletal muscle tissue development / cellular response to epidermal growth factor stimulus / 髄鞘 / transmembrane receptor protein tyrosine kinase activity / 神経発生 / basal plasma membrane / regulation of ERK1 and ERK2 cascade / response to progesterone / positive regulation of translation / liver development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of epithelial cell proliferation / Hsp90 protein binding / neuromuscular junction / wound healing / receptor tyrosine kinase binding / 受容体型チロシンキナーゼ / neuron differentiation / cellular response to growth factor stimulus / ruffle membrane / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane signaling receptor activity / presynaptic membrane / 髄鞘 / nervous system development / regulation of cell population proliferation / heart development / cytoplasmic vesicle / postsynaptic membrane / positive regulation of cell growth / basolateral plasma membrane / protein tyrosine kinase activity / positive regulation of MAPK cascade / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / エンドソーム / endosome membrane / intracellular signal transduction / response to xenobiotic stimulus / positive regulation of protein phosphorylation / apical plasma membrane / protein heterodimerization activity / リン酸化 / signaling receptor binding / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / シグナル伝達 / DNA binding / ATP binding 類似検索 - 分子機能 | |||||||||
生物種 | Rattus norvegicus (ドブネズミ) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å | |||||||||
データ登録者 | Cho, H.-S. / Mason, K. / Ramyar, K.X. / Stanley, A.M. / Gabelli, S.B. / Denney Jr., D.W. / Leahy, D.J. | |||||||||
引用 | ジャーナル: Nature / 年: 2003 タイトル: Structure of the Extracellular Region of HER2 Alone and in complex with the Herceptin Fab 著者: Cho, H.-S. / Mason, K. / Ramyar, K.X. / Stanley, A.M. / Gabelli, S.B. / Denney Jr., D.W. / Leahy, D.J. | |||||||||
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 | 1n8y.cif.gz | 130.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1n8y.ent.gz | 99.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1n8y.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/n8/1n8y ftp://data.pdbj.org/pub/pdb/validation_reports/n8/1n8y | HTTPS FTP |
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-関連構造データ
-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: 67361.422 Da / 分子数: 1 / 断片: extracellular region (residues 26-633) / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: neu / プラスミド: pSGHV0 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 株 (発現宿主): CHO(Lec1) / 参照: GenBank: 22651765, UniProt: P06494*PLUS | ||||
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#2: 多糖 | #3: 糖 | ChemComp-NAG / | #4: 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: 3.18 Å3/Da / 溶媒含有率: 61.05 % | ||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.4 詳細: 15-30% PEG4000, 50mM Na citrate pH5.4, 10mM EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 110 K |
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放射光源 | 由来: シンクロトロン / サイト: NSLS / ビームライン: X4A |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2001年2月20日 |
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 | 相対比: 1 |
反射 | 解像度: 2.4→20 Å / Num. all: 34177 / Num. obs: 33900 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / 冗長度: 5.7 % |
反射 シェル | 解像度: 2.4→2.49 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.77 / % possible all: 93.9 |
反射 | *PLUS 最低解像度: 30 Å / Num. obs: 34177 / 冗長度: 3.7 % / Num. measured all: 196228 / Rmerge(I) obs: 0.062 |
反射 シェル | *PLUS % possible obs: 93.9 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.9 |
-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: PDB entry 1M6B 解像度: 2.4→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.33 / SU ML: 0.215 / 交差検証法: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.364 / ESU R Free: 0.28
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 27.924 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.4→20 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.4→2.461 Å / Total num. of bins used: 20 /
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精密化 | *PLUS 最低解像度: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.226 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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