+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1lf5 | |||||||||
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タイトル | Crystal Structure of RasA59G in the GDP-bound Form | |||||||||
要素 | Transforming protein P21/H-RAS-1 | |||||||||
キーワード | SIGNALING PROTEIN / Ras / GTPase (GTPアーゼ) / GDP | |||||||||
機能・相同性 | 機能・相同性情報 GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / 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 / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / positive regulation of protein targeting to membrane / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Schwann cell development / 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 FLT3 ITD and TKD mutants / 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 / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / 髄鞘 / 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 / 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 / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / RAF activation / positive regulation of MAP kinase activity / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / 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 / 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 / 走化性 / 分裂促進因子活性化タンパク質キナーゼ / positive regulation of type II interferon production / 細胞老化 / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants 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: 1.7 Å | |||||||||
データ登録者 | Hall, B.E. / Bar-Sagi, D. / Nassar, N. | |||||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2002 タイトル: The Structural Basis for the Transition from Ras-GTP to Ras-GDP 著者: Hall, B.E. / Bar-Sagi, D. / Nassar, N. | |||||||||
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 | 1lf5.cif.gz | 51 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1lf5.ent.gz | 35.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1lf5.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/lf/1lf5 ftp://data.pdbj.org/pub/pdb/validation_reports/lf/1lf5 | 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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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 18861.166 Da / 分子数: 1 / 断片: Residues 1-166 / 変異: A59G / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pProEX HTb / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21 (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P01112 |
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#2: 化合物 | ChemComp-MG / |
#3: 化合物 | ChemComp-GDP / |
#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: 2.66 Å3/Da / 溶媒含有率: 53.76 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: PEG8000, calcium acetate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: NSLS / ビームライン: X26C / 波長: 1.1 Å |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2002年4月18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: 1.1 Å / 相対比: 1 |
反射 | 解像度: 1.7→20 Å / Num. obs: 267511 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / 冗長度: 12.2 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 10 |
反射 シェル | 解像度: 1.7→1.74 Å / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 2 / Rsym value: 0.196 / % possible all: 89.4 |
反射 | *PLUS 最高解像度: 1.7 Å / Num. obs: 21891 / Num. measured all: 267511 / Rmerge(I) obs: 0.054 |
反射 シェル | *PLUS % possible obs: 89.4 % / Rmerge(I) obs: 0.196 |
-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 4Q21 解像度: 1.7→19.88 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 19418557.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 74.1646 Å2 / ksol: 0.402597 e/Å3 | ||||||||||||||||||||
原子変位パラメータ | Biso mean: 30 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 1.7→19.88 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.7→1.81 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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精密化 | *PLUS 最高解像度: 1.7 Å / 最低解像度: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.222 | ||||||||||||||||||||
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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LS精密化 シェル | *PLUS Rfactor Rfree: 0.319 / Rfactor Rwork: 0.266 |