+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2nz8 | ||||||
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タイトル | N-terminal DHPH cassette of Trio in complex with nucleotide-free Rac1 | ||||||
要素 |
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キーワード | SIGNALING PROTEIN / CELL CYCLE (細胞周期) / Trio / Rac1 (RAC1) / Dbl-family GEF / Rho-family GTPase / DH/PH cassette | ||||||
機能・相同性 | 機能・相同性情報 cell surface receptor protein tyrosine phosphatase signaling pathway / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly ...cell surface receptor protein tyrosine phosphatase signaling pathway / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / respiratory burst / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / negative regulation of fat cell differentiation / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / extrinsic component of membrane / Activation of RAC1 downstream of NMDARs / Rho GDP-dissociation inhibitor binding / small GTPase-mediated signal transduction / postsynaptic modulation of chemical synaptic transmission / presynaptic active zone / NRAGE signals death through JNK / Rac protein signal transduction / RHOJ GTPase cycle / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / cell chemotaxis / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / 低分子量GTPアーゼ / neuron projection morphogenesis / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1 / cell projection / actin filament organization / 運動性 / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane 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 | Chhatriwala, M.K. / Betts, L. / Worthylake, D.K. / Sondek, J. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2007 タイトル: The DH and PH Domains of Trio Coordinately Engage Rho GTPases for their Efficient Activation 著者: Chhatriwala, M.K. / Betts, L. / Worthylake, D.K. / Sondek, J. | ||||||
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 | 2nz8.cif.gz | 210.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2nz8.ent.gz | 168.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2nz8.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/nz/2nz8 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/2nz8 | 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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詳細 | There is one biological unit in each assymetric unit (complex between Rac1 and Trio DH/PH) |
-要素
#1: タンパク質 | 分子量: 19710.764 Da / 分子数: 1 / 断片: soluble part (residues 1-177) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RAC1 / プラスミド: pET15b / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: P63000 |
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#2: タンパク質 | 分子量: 36561.953 Da / 分子数: 1 / 断片: N-terminal DH/PH cassette (residues 1226-1535) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRIO / プラスミド: pPROEX-HTa / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: O75962 |
#3: 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: 2.51 Å3/Da / 溶媒含有率: 51.01 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法 / pH: 6 詳細: 100 mM sodium cacodylate pH 5.5 to 6.5, 14 to 18% (w/v) PEG 8000, and 300-500 mM calcium acetate, pH 6.0, VAPOR DIFFUSION, temperature 291K |
-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: APS / ビームライン: 22-ID / 波長: 1.0712 Å |
検出器 | タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2004年10月29日 |
放射 | モノクロメーター: double crystal Si (220) cryogenically cooled monochromator 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: 1.0712 Å / 相対比: 1 |
反射 | 解像度: 2→20 Å / Num. all: 39574 / Num. obs: 39416 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / 冗長度: 5.4 % / Rsym value: 0.069 / Χ2: 1.824 / Net I/σ(I): 15.6 |
反射 シェル | 解像度: 2→2.07 Å / 冗長度: 4.2 % / Mean I/σ(I) obs: 3.53 / Num. unique all: 3903 / Rsym value: 0.524 / Χ2: 1.124 / % possible all: 99.8 |
-位相決定
Phasing MR |
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-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: residues 1231-1390 of PDB entry 1NTY and residues 1-177 of PDB entry 1FOE 解像度: 2→19.41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.565 / SU ML: 0.111 / Isotropic thermal model: isotropic / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.165 / 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: 41.241 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2→19.41 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2→2.051 Å / Total num. of bins used: 20
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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