+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1rvd | ||||||
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タイトル | H-RAS COMPLEXED WITH DIAMINOBENZOPHENONE-BETA,GAMMA-IMIDO-GTP | ||||||
要素 | TRANSFORMING PROTEIN P21/H-RAS-1 | ||||||
キーワード | HYDROLASE (加水分解酵素) / GTP HYDROLASE / SIGNAL TRANSDUCTION (シグナル伝達) / CANCER (悪性腫瘍) / G-DOMAIN (ゴールドマン整域) | ||||||
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 / positive regulation of phospholipase C activity / 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 / protein-membrane adaptor activity / 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 / 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 / 髄鞘 / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / 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 / regulation of long-term neuronal synaptic plasticity / animal organ morphogenesis / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / cellular response to gamma radiation / Constitutive Signaling by EGFRvIII / 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 | X線回折 / 分子置換 / 解像度: 1.9 Å | ||||||
データ登録者 | Ahmadian, M.R. / Zor, T. / Vogt, D. / Kabsch, W. / Selinger, Z. / Wittinghofer, A. / Scheffzek, K. | ||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 1999 タイトル: Guanosine triphosphatase stimulation of oncogenic Ras mutants. 著者: Ahmadian, M.R. / Zor, T. / Vogt, D. / Kabsch, W. / Selinger, Z. / Wittinghofer, A. / Scheffzek, K. #1: ジャーナル: Febs Lett. / 年: 1998 タイトル: GTP analogue hydrolysis by the Gs protein: implication for the role of catalytic glutamine in the GTPase reaction. 著者: Zor, T. / Andorn, R. / Sofer, I. / Chorev, M. / Selinger, Z. #2: ジャーナル: Eur.J.Biochem. / 年: 1997 タイトル: Rescue of a mutant G-protein by substrate-assisted catalysis. 著者: Zor, T. / Bar-Yaacov, M. / Elgavish, S. / Shaanan, B. / Selinger, Z. #3: ジャーナル: Biochemistry / 年: 1993 タイトル: Three-dimensional structures and properties of a transforming and a nontransforming glycine-12 mutant of p21H-ras. 著者: Franken, S.M. / Scheidig, A.J. / Krengel, U. / Rensland, H. / Lautwein, A. / Geyer, M. / Scheffzek, K. / Goody, R.S. / Kalbitzer, H.R. / Pai, E.F. #4: ジャーナル: Cell(Cambridge,Mass.) / 年: 1990 タイトル: Three-dimensional structures of H-ras p21 mutants: molecular basis for their inability to function as signal switch molecules. 著者: Krengel, U. / Schlichting, I. / Scherer, A. / Schumann, R. / Frech, M. / John, J. / Kabsch, W. / Pai, E.F. / Wittinghofer, 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 | 1rvd.cif.gz | 48.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1rvd.ent.gz | 32.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1rvd.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/rv/1rvd ftp://data.pdbj.org/pub/pdb/validation_reports/rv/1rvd | 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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単位格子 |
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-要素
#1: タンパク質 | 分子量: 18917.271 Da / 分子数: 1 / 断片: CATALYTIC DOMAIN, RESIDUES 1 - 166 / 変異: GLY12VAL / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 参照: UniProt: P01112 |
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#2: 化合物 | ChemComp-MG / |
#3: 化合物 | ChemComp-DBG / |
#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: 2 Å3/Da / 溶媒含有率: 30 % | ||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: SEE REFERENCE DECRIBING THE STRUCTURE AND CITATIONS THEREIN, pH 7.5, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: batch method | ||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 277 K |
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放射光源 | 由来: 回転陽極 / タイプ: ELLIOTT GX-18 / 波長: 1.5418 |
検出器 | タイプ: SIEMENS / 検出器: AREA DETECTOR / 日付: 1998年4月15日 / 詳細: MIRRORS |
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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 1.9→100 Å / % possible obs: 98.7 % / 冗長度: 6.5 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 9 / Net I/σ(I): 15.3 |
反射 シェル | 解像度: 1.8→1.9 Å / 冗長度: 3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.5 / Rsym value: 33 / % possible all: 93.3 |
反射 | *PLUS Num. obs: 12666 / Num. measured all: 83084 |
反射 シェル | *PLUS % possible obs: 93.3 % |
-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: 5P21 解像度: 1.9→5 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0
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原子変位パラメータ | Biso mean: 17.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 1.9→5 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.9→2.01 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.851 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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