+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5ovd | ||||||
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タイトル | Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in new crystal form | ||||||
要素 | Son of sevenless homolog 1 | ||||||
キーワード | SIGNALING PROTEIN / Guanine exchange factor (グアニンヌクレオチド交換因子) / GEF / inhibitor (酵素阻害剤) / SOS1 | ||||||
機能・相同性 | 機能・相同性情報 midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling ...midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / blood vessel morphogenesis / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / epidermal growth factor receptor binding / leukocyte migration / NRAGE signals death through JNK / regulation of T cell proliferation / roof of mouth development / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / SOS-mediated signalling / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / Signalling to RAS / fibroblast growth factor receptor signaling pathway / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / 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 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / RAC1 GTPase cycle / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / 髄鞘 / Signaling by FLT3 fusion proteins / FLT3 Signaling / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / GTPase activator activity / SHC1 events in ERBB2 signaling / molecular condensate scaffold activity / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / guanyl-nucleotide exchange factor activity / insulin-like growth factor receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to ischemia / 軸索誘導 / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / B cell receptor signaling pathway / multicellular organism growth / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / SH3 domain binding / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / G alpha (12/13) signalling events / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / insulin receptor signaling pathway / regulation of cell population proliferation / RAF/MAP kinase cascade / Ras protein signal transduction / Potential therapeutics for SARS / protein heterodimerization activity / neuronal cell body 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: 1.9 Å | ||||||
データ登録者 | Hillig, R.C. / Moosmayer, D. / Hilpmann, A. / Bader, B. / Schroeder, J. / Wortmann, L. / Sautier, B. / Kahmann, J. / Wegener, D. / Briem, H. ...Hillig, R.C. / Moosmayer, D. / Hilpmann, A. / Bader, B. / Schroeder, J. / Wortmann, L. / Sautier, B. / Kahmann, J. / Wegener, D. / Briem, H. / Petersen, K. / Badock, V. | ||||||
引用 | ジャーナル: Proc. Natl. Acad. Sci. U.S.A. / 年: 2019 タイトル: Discovery of potent SOS1 inhibitors that block RAS activation via disruption of the RAS-SOS1 interaction. 著者: Hillig, R.C. / Sautier, B. / Schroeder, J. / Moosmayer, D. / Hilpmann, A. / Stegmann, C.M. / Werbeck, N.D. / Briem, H. / Boemer, U. / Weiske, J. / Badock, V. / Mastouri, J. / Petersen, K. / ...著者: Hillig, R.C. / Sautier, B. / Schroeder, J. / Moosmayer, D. / Hilpmann, A. / Stegmann, C.M. / Werbeck, N.D. / Briem, H. / Boemer, U. / Weiske, J. / Badock, V. / Mastouri, J. / Petersen, K. / Siemeister, G. / Kahmann, J.D. / Wegener, D. / Bohnke, N. / Eis, K. / Graham, K. / Wortmann, L. / von Nussbaum, F. / Bader, B. | ||||||
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 | 5ovd.cif.gz | 217.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5ovd.ent.gz | 173.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5ovd.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/ov/5ovd ftp://data.pdbj.org/pub/pdb/validation_reports/ov/5ovd | HTTPS FTP |
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-関連構造データ
関連構造データ | 5oveC 5ovfC 5ovgC 5ovhC 5oviC 6eieC 6eplC 6epmC 6epnC 6epoC 6eppC 2ii0S S: 精密化の開始モデル C: 同じ文献を引用 (文献) |
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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: 57376.637 Da / 分子数: 1 / 変異: Q560G, E561A, E562M, K563A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SOS1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q07889 | ||
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#2: 化合物 | ChemComp-EDO / #3: 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: 2.68 Å3/Da / 溶媒含有率: 54.14 % |
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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: 7.5 詳細: Protein concentration 30.7 mg/ml. Protein buffer 25 Millimolar TRIS-HCL PH 7.5, 50 millimolar NaCl, 1 millimolar DTT. Reservoir 23% (v/v) ethylenglycol. No cryo required as grown from ethylenglycol as precipitant |
-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: シンクロトロン / サイト: BESSY / ビームライン: 14.1 / 波長: 0.9184 Å |
検出器 | タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2017年8月9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 | 波長: 0.9184 Å / 相対比: 1 |
反射 | 解像度: 1.9→48.37 Å / Num. obs: 49297 / % possible obs: 98.7 % / 冗長度: 4.79 % / Biso Wilson estimate: 43.44 Å2 / CC1/2: 0.999 / Rsym value: 0.06 / Net I/σ(I): 13.99 |
反射 シェル | 解像度: 1.9→2.01 Å / 冗長度: 4.87 % / Mean I/σ(I) obs: 1.46 / Num. unique obs: 7749 / CC1/2: 0.678 / Rsym value: 1.052 / % possible all: 97.6 |
-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: 2ii0 解像度: 1.9→48.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.237 / SU ML: 0.119 / 交差検証法: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.14 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 1.2 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 54.861 Å2
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精密化ステップ | サイクル: 1 / 解像度: 1.9→48.37 Å
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拘束条件 |
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