+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6mqn | ||||||
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タイトル | Crystal structure of KRAS V14I-GDP demonstrating disorder switch 1 conformation - Form 2 | ||||||
要素 | GTPase KRas | ||||||
キーワード | HYDROLASE (加水分解酵素) / GTPASE KRAS HYDROLYSIS | ||||||
機能・相同性 | 機能・相同性情報 forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / 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 / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / 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 CSF3 (G-CSF) / positive regulation of glial cell proliferation / Signaling by FLT3 ITD and TKD mutants / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / 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 / 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 / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / Signaling by RAF1 mutants / GDP binding / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by CSF1 (M-CSF) in myeloid cells / 分裂促進因子活性化タンパク質キナーゼ / Signaling by BRAF and RAF1 fusions / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Ca2+ pathway / 遺伝子発現 / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / mitochondrial outer membrane / negative regulation of neuron apoptotic process / Ras protein signal transduction / positive regulation of protein phosphorylation / ゴルジ体 / focal 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: 1.6 Å | ||||||
データ登録者 | Bera, A.K. / Westover, K.D. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 2019 タイトル: Structural basis of the atypical activation mechanism of KRASV14I. 著者: Bera, A.K. / Lu, J. / Wales, T.E. / Gondi, S. / Gurbani, D. / Nelson, A. / Engen, J.R. / Westover, K.D. | ||||||
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 | 6mqn.cif.gz | 299.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6mqn.ent.gz | 247.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6mqn.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/mq/6mqn ftp://data.pdbj.org/pub/pdb/validation_reports/mq/6mqn | 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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2 |
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3 |
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単位格子 |
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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 19285.785 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KRAS, KRAS2, RASK2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01116 #2: 化合物 | #3: 水 | ChemComp-HOH / | |
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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: 2.05 Å3/Da / 溶媒含有率: 39.87 % |
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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: 8.2 / 詳細: 1.8M Na/K Phosphate pH 8.2 |
-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: 19-ID / 波長: 0.9795 Å |
検出器 | タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2018年4月12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: 0.9795 Å / 相対比: 1 |
反射 | 解像度: 1.6→50 Å / Num. obs: 59738 / % possible obs: 98.1 % / 冗長度: 6.5 % / CC1/2: 0.84 / Rpim(I) all: 0.025 / Net I/av σ(I): 28.5 / Net I/σ(I): 28.5 |
反射 シェル | 解像度: 1.6→1.63 Å / 冗長度: 4.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2797 / CC1/2: 0.57 / Rpim(I) all: 0.447 / % possible all: 91.3 |
-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: 4OBE 解像度: 1.6→42.112 Å / SU ML: 0.17 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 23.49
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 90.85 Å2 / Biso mean: 22.728 Å2 / Biso min: 1.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 1.6→42.112 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: 20
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精密化 TLS | 手法: refined / Origin x: 31.4928 Å / Origin y: 3.8483 Å / Origin z: 22.0636 Å
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精密化 TLSグループ |
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