+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2uzi | ||||||
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タイトル | Crystal structure of HRAS(G12V) - anti-RAS Fv complex | ||||||
要素 |
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キーワード | SIGNALING PROTEIN/IMMUNE SYSTEM / SIGNAL TRANSDUCTION (シグナル伝達) / IMMUNOGLOBULIN DOMAIN (免疫グロブリンフォールド) / MEMBRANE (生体膜) / ANTIBODY (抗体) / ONCOGENE (がん遺伝子) / PALMITATE (パルミチン酸) / INTRABODY / DISEASE MUTATION / NUCLEOTIDE-BINDING / PROTO-ONCOGENE (がん遺伝子) / CANCER THERAPY (悪性腫瘍) / GOLGI APPARATUS (ゴルジ体) / PRENYLATION (プレニル化) / METHYLATION (メチル化) / LIPOPROTEIN (リポタンパク質) / GTP- BINDING / SIGNALING PROTEIN-IMMUNE SYSTEM complex | ||||||
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 / positive regulation of JNK cascade / animal organ morphogenesis / regulation of long-term neuronal synaptic plasticity / 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 / シンクロトロン / 分子置換 / 解像度: 2 Å | ||||||
データ登録者 | Tanaka, T. / williams, R.L. / Rabbitts, T.H. | ||||||
引用 | ジャーナル: Embo J. / 年: 2007 タイトル: Tumour Prevention by a Single Antibody Domain Targeting the Interaction of Signal Transduction Proteins with Ras. 著者: Tanaka, T. / Williams, R.L. / Rabbitts, T.H. | ||||||
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 | 2uzi.cif.gz | 100.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2uzi.ent.gz | 74.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2uzi.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/uz/2uzi ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uzi | 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
-タンパク質 , 1種, 1分子 R
#3: タンパク質 | 分子量: 18917.271 Da / 分子数: 1 / Fragment: RESIDUES 1-166 / Mutation: YES / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PRK172 / 発現宿主: ESCHERICHIA COLI BL21(DE3) (大腸菌) / Variant (発現宿主): C41 / 参照: UniProt: P01112 |
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-抗体 , 2種, 2分子 HL
#1: 抗体 | 分子量: 12688.229 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PRK-HISTEV-VH-RAS-VL / 発現宿主: ESCHERICHIA COLI BL21(DE3) (大腸菌) / Variant (発現宿主): C41 |
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#2: 抗体 | 分子量: 11220.517 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PRK-HISTEV-VH-RAS-VL / 発現宿主: ESCHERICHIA COLI BL21(DE3) (大腸菌) / Variant (発現宿主): C41 |
-非ポリマー , 4種, 296分子
#4: 化合物 | ChemComp-ZN / #5: 化合物 | ChemComp-GTP / | #6: 化合物 | ChemComp-MG / | #7: 水 | ChemComp-HOH / | |
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-詳細
構成要素の詳細 | ENGINEERED |
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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: 2.15 Å3/Da / 溶媒含有率: 38.2 % |
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結晶化 | 詳細: PROTEIN WAS CRYSTALLIZED FROM 17-18 % PEG3350, 400 MM ZINC ACETATE, 100 MM SODIUM CACODYLATE, PH 5.8, 0.03 % DICHLOROMETHANE |
-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: ESRF / ビームライン: ID14-4 / 波長: 0.934 |
検出器 | タイプ: ADSC CCD / 検出器: CCD / 日付: 2005年11月11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: 0.934 Å / 相対比: 1 |
反射 | 解像度: 2→50.32 Å / Num. obs: 27214 / % possible obs: 98.2 % / Observed criterion σ(I): 3.7 / 冗長度: 3.38 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.42 |
反射 シェル | 解像度: 2→2.02 Å / 冗長度: 3.35 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.67 / % possible all: 97.2 |
-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 1AGP, 1A2Y 解像度: 2→41.89 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.894 / SU B: 4.749 / SU ML: 0.136 / 交差検証法: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.2 / 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: 24.27 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2→41.89 Å
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拘束条件 |
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