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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 7qsc | ||||||
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タイトル | GTPase IN COMPLEX WITH GDP.MGF3- | ||||||
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![]() | HYDROLASE / Small G Protein / GTPase / Transition state analogue / metal fluoride complexes / fluoro-tyrosine | ||||||
機能・相同性 | ![]() negative regulation of endocytic recycling / transferrin transport / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction ...negative regulation of endocytic recycling / transferrin transport / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / negative regulation of cell size / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / RHOF GTPase cycle / negative regulation of motor neuron apoptotic process / RHOD GTPase cycle / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / regulation of small GTPase mediated signal transduction / positive regulation of alpha-beta T cell differentiation / ossification involved in bone maturation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / motor neuron apoptotic process / RND2 GTPase cycle / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / wound healing, spreading of cells / apical junction complex / regulation of neuron projection development / regulation of focal adhesion assembly / endosomal transport / negative chemotaxis / RHOB GTPase cycle / small GTPase-mediated signal transduction / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / positive regulation of cytokinesis / cerebral cortex cell migration / androgen receptor signaling pathway / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / CDC42 GTPase cycle / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / RHOG GTPase cycle / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / skeletal muscle tissue development / RHO GTPases activate PKNs / regulation of cell migration / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / GTPase activator activity / cell-matrix adhesion 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Baumann, P. / Jin, Y. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: GTPase IN COMPLEX WITH GDP.MGF3- 著者: Baumann, P. / Jin, Y. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 169.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 130.7 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 2.6 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2.6 MB | 表示 | |
XML形式データ | ![]() | 31.7 KB | 表示 | |
CIF形式データ | ![]() | 44.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 5m6xS S: 精密化の開始モデル |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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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 , 2種, 4分子 ACBD
#1: タンパク質 | 分子量: 27502.482 Da / 分子数: 2 / 変異: R85A / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 21688.863 Da / 分子数: 2 / 変異: Y34(F3Y) / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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-非ポリマー , 4種, 319分子 ![](data/chem/img/GDP.gif)
![](data/chem/img/MGF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MGF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: 化合物 | #4: 化合物 | #5: 化合物 | #6: 水 | ChemComp-HOH / | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 1.93 Å3/Da / 溶媒含有率: 36.34 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6 詳細: Protein stock of RhoA-Y34F3Y 0.7 mM, RhoGAP-R85A 0.7 mM in a buffer of BisTris-HCl, pH 6.0, NaCl 150 mM, MgCl2 5 mM, NaF 10 mM, DTT 1 mM mixed 1:1.2 ratio with the precipitant solution of 0.1 ...詳細: Protein stock of RhoA-Y34F3Y 0.7 mM, RhoGAP-R85A 0.7 mM in a buffer of BisTris-HCl, pH 6.0, NaCl 150 mM, MgCl2 5 mM, NaF 10 mM, DTT 1 mM mixed 1:1.2 ratio with the precipitant solution of 0.1 M BisTris-HCl, pH 5.8, PEG3350 26% (w/v). |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2020年10月22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: 0.9763 Å / 相対比: 1 |
反射 | 解像度: 1.91→55.64 Å / Num. obs: 57691 / % possible obs: 100 % / 冗長度: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.085 / Rrim(I) all: 0.16 / Net I/σ(I): 10.4 |
反射 シェル | 解像度: 1.91→1.95 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3865 / CC1/2: 0.649 / % possible all: 100 |
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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: ![]() 開始モデル: 5M6X 解像度: 1.91→55.64 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.572 / SU ML: 0.183 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.194 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 73.99 Å2 / Biso mean: 28.051 Å2 / Biso min: 0.5 Å2
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精密化ステップ | サイクル: final / 解像度: 1.91→55.64 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.91→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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