+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2vh5 | ||||||
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タイトル | CRYSTAL STRUCTURE OF HRAS(G12V) - ANTI-RAS FV (disulfide free mutant) COMPLEX | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / IMMUNOGLOBULIN DOMAIN (免疫グロブリンフォールド) / SIGNALING PROTEIN/IMMUNE SYSTEM / METHYLATION (メチル化) / PRENYLATION (プレニル化) / LIPOPROTEIN (リポタンパク質) / GTP-BINDING / SIGNAL TRANSDUCTION (シグナル伝達) / NUCLEOTIDE- BINDING / DISEASE MUTATION / NUCLEOTIDE-BINDING / MEMBRANE (生体膜) / ONCOGENE (がん遺伝子) / ANTIBODY (抗体) / PALMITATE (パルミチン酸) / INTRABODY / PROTO-ONCOGENE (がん遺伝子) / CANCER THERAPY (悪性腫瘍) / GOLGI APPARATUS (ゴルジ体) | ||||||
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 / その他 / 解像度: 2.7 Å | ||||||
データ登録者 | Tanaka, T. / Williams, R.L. / Rabbitts, T.H. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2008 タイトル: Functional Intracellular Antibody Fragments Do not Require Invariant Intra-Domain Disulfide Bonds. 著者: Tanaka, T. / Rabbitts, T.H. #1: 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 | 2vh5.cif.gz | 86.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2vh5.ent.gz | 69.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2vh5.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/vh/2vh5 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/2vh5 | HTTPS FTP |
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-関連構造データ
関連構造データ | |
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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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単位格子 |
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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: PRK-HISTEV-VH-RAS-VL / 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: 12652.152 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: 11184.439 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, 47分子
#4: 化合物 | #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: 2.39 Å3/Da / 溶媒含有率: 48.53 % / 解説: NONE |
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結晶化 | pH: 5.8 詳細: PROTEIN WAS CRYSTALLIZED FROM 17-18 % PEG3350, 320 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: 回転陽極 / タイプ: RIGAKU RUH3R / 波長: 1.5418 |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2005年12月8日 / 詳細: OSMIC CONFOCAL OPTICS |
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: 2.7→42.18 Å / Num. obs: 11682 / % possible obs: 99.5 % / Observed criterion σ(I): 3.7 / 冗長度: 4.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.4 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: その他 開始モデル: NONE 解像度: 2.7→42.18 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.844 / SU B: 31.53 / SU ML: 0.332 / 交差検証法: THROUGHOUT / ESU R Free: 0.422 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 40.76 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.7→42.18 Å
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拘束条件 |
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