+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5zc6 | |||||||||
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タイトル | Solution structure of H-RasT35S mutant protein in complex with KBFM123 | |||||||||
要素 | GTPase HRasHRAS | |||||||||
キーワード | ONCOPROTEIN (がん遺伝子) / Inhibitor / Complex / Cancer (悪性腫瘍) / Small GTPases (低分子量GTPアーゼ) | |||||||||
機能・相同性 | 機能・相同性情報 GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / 髄鞘 / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / 低分子量GTPアーゼ / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / Signaling by ERBB2 TMD/JMD mutants / positive regulation of JNK cascade / regulation of long-term neuronal synaptic plasticity / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / cellular response to gamma radiation / positive regulation of MAP kinase activity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / positive regulation of GTPase activity / エンドサイトーシス / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / 走化性 / positive regulation of fibroblast proliferation / 分裂促進因子活性化タンパク質キナーゼ / 細胞老化 / Signaling by BRAF and RAF1 fusions / positive regulation of type II interferon production / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 溶液NMR / simulated annealing | |||||||||
データ登録者 | Matsumoto, S. / Hayashi, Y. / Hiraga, T. / Matsuo, K. / Kataoka, T. | |||||||||
資金援助 | 日本, 2件
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引用 | ジャーナル: Biochemistry / 年: 2018 タイトル: Molecular Basis for Allosteric Inhibition of GTP-Bound H-Ras Protein by a Small-Molecule Compound Carrying a Naphthalene Ring 著者: Matsumoto, S. / Hiraga, T. / Hayashi, Y. / Yoshikawa, Y. / Tsuda, C. / Araki, M. / Neya, M. / Shima, F. / Kataoka, T. | |||||||||
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 | 5zc6.cif.gz | 800.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5zc6.ent.gz | 659.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5zc6.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/zc/5zc6 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/5zc6 | HTTPS FTP |
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-関連構造データ
関連構造データ | |
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類似構造データ | |
その他のデータベース |
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-リンク
-集合体
登録構造単位 |
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1 |
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NMR アンサンブル |
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-要素
#1: タンパク質 | 分子量: 18861.166 Da / 分子数: 1 / 断片: UNP residues 1-166 / 変異: T35S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HRAS, HRAS1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01112 |
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#2: 化合物 | ChemComp-GNP / |
#3: 化合物 | ChemComp-KBF / |
#4: 化合物 | ChemComp-MG / |
-実験情報
-実験
実験 | 手法: 溶液NMR | ||||||||||||||||||||||||
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NMR実験 |
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-試料調製
詳細 | タイプ: solution 内容: 0.8 mM [U-99% 13C; U-99% 15N] H-RasT35S, 3.0 mM KBFM123, 20 mM sodium phosphate, 40 mM sodium chloride, 8 mM MAGNESIUM ION, 0.8 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, 80% D2O/20% d6-DMSO Label: sample_1 / 溶媒系: 80% D2O/20% d6-DMSO | ||||||||||||||||||||||||||||
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試料 |
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試料状態 | イオン強度: 50 mM / Label: conditions_1 / pH: 6.8 / 圧: ambient Pa / 温度: 278 K |
-NMR測定
NMRスペクトロメーター | タイプ: Bruker AVANCE III / 製造業者: Bruker / モデル: AVANCE III / 磁場強度: 600 MHz |
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-解析
NMR software | 名称: CNS / 開発者: BRUNGER A. T. ET.AL. / 分類: 精密化 |
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精密化 | 手法: simulated annealing / ソフトェア番号: 1 |
代表構造 | 選択基準: lowest energy |
NMRアンサンブル | コンフォーマー選択の基準: structures with the lowest energy 計算したコンフォーマーの数: 100 / 登録したコンフォーマーの数: 15 |