+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2wkr | ||||||
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タイトル | Structure of a photoactivatable Rac1 containing the Lov2 C450M Mutant | ||||||
要素 | NPH1-1, RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 | ||||||
キーワード | TRANSFERASE (転移酵素) / CELL ADHESION (細胞接着) / NUCLEOTIDE-BINDING / PROTEIN ENGINEERING (タンパク質工学) / RAS SUPERFAMILY LOV2 / PHOTOTROPIN1 / PROTEIN DESIGN (タンパク質設計) / SMALL G-PROTEIN (低分子量GTPアーゼ) / LIGHT-INDUCED SIGNAL TRANSDUCTION / GTPASE (GTPアーゼ) / RHO FAMILY (RhoファミリーGタンパク質) / ATP-BINDING / PRENYLATION (プレニル化) / CHIMERA / NUCLEOTIDE-BINDING PROTEIN ENGINEERING / ADP-RIBOSYLATION (ADPリボース化) | ||||||
機能・相同性 | 機能・相同性情報 regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / blue light photoreceptor activity / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 ...regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / blue light photoreceptor activity / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / ruffle organization / thioesterase binding / negative regulation of fibroblast migration / cell projection assembly / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / regulation of nitric oxide biosynthetic process / PCP/CE pathway / RHO GTPases activate KTN1 / motor neuron axon guidance / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / regulation of lamellipodium assembly / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / regulation of cell size / DSCAM interactions / Activation of RAC1 downstream of NMDARs / establishment or maintenance of cell polarity / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / positive regulation of Rho protein signal transduction / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RHO GTPases activate IQGAPs / localization / positive regulation of lamellipodium assembly / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / positive regulation of microtubule polymerization / regulation of cell migration / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / positive regulation of endothelial cell migration / cell chemotaxis / substrate adhesion-dependent cell spreading / cell-matrix adhesion / 低分子量GTPアーゼ / secretory granule membrane / G protein activity / VEGFR2 mediated vascular permeability / Signal transduction by L1 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / 運動性 / actin filament organization / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / neuron migration / MAPK6/MAPK4 signaling / ゴルジ体 / Signaling by SCF-KIT / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / VEGFA-VEGFR2 Pathway / response to wounding / cytoplasmic ribonucleoprotein granule / recycling endosome membrane / Constitutive Signaling by Aberrant PI3K in Cancer 類似検索 - 分子機能 | ||||||
生物種 | AVENA SATIVA (エンバク) HOMO SAPIENS (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.2 Å | ||||||
データ登録者 | Wu, Y.I. / Frey, D. / Lungu, O.I. / Jaehrig, A. / Schlichting, I. / Kuhlman, B. / Hahn, K.M. | ||||||
引用 | ジャーナル: Nature / 年: 2009 タイトル: A Genetically Encoded Photoactivatable Rac Controls the Motility of Living Cells. 著者: Wu, Y.I. / Frey, D. / Lungu, O.I. / Jaehrig, A. / Schlichting, I. / Kuhlman, B. / Hahn, K.M. | ||||||
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 | 2wkr.cif.gz | 87.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2wkr.ent.gz | 63.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2wkr.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/wk/2wkr ftp://data.pdbj.org/pub/pdb/validation_reports/wk/2wkr | 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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-要素
-タンパク質 , 1種, 1分子 A
#1: タンパク質 | 分子量: 37631.035 Da / 分子数: 1 断片: NPH1-1, RESIDUES 404-546 AND P21-RAC1, RESIDUES 4-180 変異: YES / 由来タイプ: 組換発現 由来: (組換発現) AVENA SATIVA (エンバク), (組換発現) HOMO SAPIENS (ヒト) プラスミド: PQE30 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): XL10 GOLD / 参照: UniProt: O49003, UniProt: P63000 |
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-非ポリマー , 5種, 220分子
#2: 化合物 | ChemComp-GTP / | ||
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#3: 化合物 | ChemComp-FMN / | ||
#4: 化合物 | ChemComp-MG / | ||
#5: 化合物 | #6: 水 | ChemComp-HOH / | |
-詳細
構成要素の詳細 | ENGINEERED RESIDUE IN CHAIN A, CYS 450 TO MET ENGINEERED RESIDUE IN CHAIN A, GLN 61 TO LEU ...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: 3.46 Å3/Da / 溶媒含有率: 64.5 % / 解説: NONE |
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結晶化 | 詳細: 18 % (V/V) PEG 600 |
-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: SLS / ビームライン: X10SA / 波長: 0.9797 |
検出器 | タイプ: MARRESEARCH MX-225 / 検出器: CCD / 日付: 2008年10月11日 |
放射 | モノクロメーター: SI(111) / 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: 0.9797 Å / 相対比: 1 |
反射 | 解像度: 2.2→50 Å / Num. obs: 25771 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / 冗長度: 3.7 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.7 |
反射 シェル | 解像度: 2.2→2.3 Å / 冗長度: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8 |
-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 ENTRIES 1MH1, 2VOU 解像度: 2.2→32.601 Å / SU ML: 0.26 / σ(F): 1.99 / 位相誤差: 20.62 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 38.656 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 22.8 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.2→32.601 Å
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拘束条件 |
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LS精密化 シェル |
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