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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: 1lb1 | ||||||
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タイトル | Crystal Structure of the Dbl and Pleckstrin homology domains of Dbs in complex with RhoA | ||||||
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![]() | SIGNALING PROTEIN / GUANINE NUCLEOTIDE EXCHANGE FACTOR / SMALL G-PROTEIN / RHOA / DBS / DH domain / PH domain | ||||||
機能・相同性 | ![]() RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / NRAGE signals death through JNK / 1-phosphatidylinositol binding / RAC1 GTPase cycle / RHOA GTPase cycle / RHOG GTPase cycle / G alpha (12/13) signalling events / aortic valve formation ...RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / NRAGE signals death through JNK / 1-phosphatidylinositol binding / RAC1 GTPase cycle / RHOA GTPase cycle / RHOG GTPase cycle / G alpha (12/13) signalling events / 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 / beta selection / establishment of epithelial cell apical/basal polarity / negative regulation of cell size / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / 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 / 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 / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / wound healing, spreading of cells / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / positive regulation of Rho protein signal transduction / extrinsic component of membrane / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / positive regulation of cytokinesis / androgen receptor signaling pathway / cerebral cortex cell migration / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / 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 / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / regulation of cell migration / substrate adhesion-dependent cell spreading / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / G protein activity / guanyl-nucleotide exchange factor activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Snyder, J.T. / Worthylake, D.K. / Rossman, K.L. / Betts, L. / Pruitt, W.M. / Siderovski, D.P. / Der, C.J. / Sondek, J. | ||||||
![]() | ![]() タイトル: Structural basis for the selective activation of Rho GTPases by Dbl exchange factors. 著者: Snyder, J.T. / Worthylake, D.K. / Rossman, K.L. / Betts, L. / Pruitt, W.M. / Siderovski, D.P. / Der, C.J. / Sondek, J. | ||||||
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 | ![]() | 364.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 305.8 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
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アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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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
#1: タンパク質 | 分子量: 41252.332 Da / 分子数: 4 断片: DBL homology domain (residues 623-818) and pleckstrin homology domain (residues 819-967) 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() #2: タンパク質 | 分子量: 21585.775 Da / 分子数: 4 / 断片: residues 1-190 / Mutation: C190S / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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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: 3.81 Å3/Da / 溶媒含有率: 67.72 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.4 詳細: PEG 3350, lithium citrate, Inositol 1,4,5-trisphosphate, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 18 ℃ / pH: 8 / 手法: 蒸気拡散法 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 80 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2002年2月15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: 0.9765 Å / 相対比: 1 |
反射 | 解像度: 2.81→47.7 Å / Num. all: 85993 / Num. obs: 85993 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 87.9 Å2 / Limit h max: 56 / Limit h min: 0 / Limit k max: 56 / Limit k min: 0 / Limit l max: 53 / Limit l min: 0 / Observed criterion F max: 2986395.32 / Observed criterion F min: 8.8 |
反射 | *PLUS 最高解像度: 2.8 Å / 最低解像度: 50 Å / Num. obs: 86038 / % possible obs: 99.1 % / Num. measured all: 269910 / Rmerge(I) obs: 0.078 |
反射 シェル | *PLUS % possible obs: 94.1 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 1.5 |
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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: Dbs-Cdc42 (pdb code 1KZ7) 解像度: 2.81→47.7 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / 交差検証法: THROUGHOUT / σ(F): 0
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溶媒の処理 | 溶媒モデル: CNS bulk solvent model used / Bsol: 45.4826 Å2 / ksol: 0.33567 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 200.54 Å2 / Biso mean: 80.6 Å2 / Biso min: 4.81 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.81→47.7 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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ソフトウェア | *PLUS 名称: CNS / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 2.8 Å / 最低解像度: 50 Å / Rfactor obs: 0.236 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.236 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.437 / Rfactor Rwork: 0.403 / Rfactor obs: 0.403 |