+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5a0f | |||||||||
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タイトル | Crystal structure of Yersinia Afp18-modified RhoA | |||||||||
要素 | TRANSFORMING PROTEIN RHOA | |||||||||
キーワード | SIGNALING PROTEIN / N-ACETYLGLUCOSAMINE-PROTEIN / TYROSINE GLYCOSYLATION / GTPASE (GTPアーゼ) / BACTERIAL TOXIN EFFECTOR / TYPE 6 SECRETION SYSTEM / ANTIFEEDING PROPHAGE | |||||||||
機能・相同性 | 機能・相同性情報 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 ...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 / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / negative regulation of cell size / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / positive regulation of alpha-beta T cell differentiation / 歯の発生 / motor neuron apoptotic process / wound healing, spreading of cells / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / 分裂溝 / 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 / cytoplasmic microtubule organization / skeletal muscle tissue development / regulation of cell migration / negative regulation of reactive oxygen species biosynthetic process / 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 / substrate adhesion-dependent cell spreading / cell-matrix adhesion / 低分子量GTPアーゼ / G protein activity / secretory granule membrane / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / neuron migration / cell morphogenesis / positive regulation of protein serine/threonine kinase activity / cytoplasmic side of plasma membrane / ruffle membrane / VEGFA-VEGFR2 Pathway / positive regulation of non-canonical NF-kappaB signal transduction / G beta:gamma signalling through PI3Kgamma / G alpha (12/13) signalling events 類似検索 - 分子機能 | |||||||||
生物種 | HOMO SAPIENS (ヒト) | |||||||||
手法 | X線回折 / 分子置換 / 解像度: 2 Å | |||||||||
データ登録者 | Jank, T. / Schimpl, M. / van Aalten, D.M. | |||||||||
引用 | ジャーナル: Nat Commun / 年: 2015 タイトル: Tyrosine glycosylation of Rho by Yersinia toxin impairs blastomere cell behaviour in zebrafish embryos. 著者: Jank, T. / Eckerle, S. / Steinemann, M. / Trillhaase, C. / Schimpl, M. / Wiese, S. / van Aalten, D.M. / Driever, W. / Aktories, K. | |||||||||
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 | 5a0f.cif.gz | 51.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5a0f.ent.gz | 36 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5a0f.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/a0/5a0f ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a0f | HTTPS FTP |
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-関連構造データ
関連構造データ | 1dpfS S: 精密化の開始モデル |
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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
#1: タンパク質 | 分子量: 20467.457 Da / 分子数: 1 / 断片: RESIDUES 1-181 / 由来タイプ: 組換発現 / 詳細: GLYCOSYLATION AT Y 34 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PGEX4T / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P61586 |
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#2: 化合物 | ChemComp-GDP / |
#3: 化合物 | ChemComp-SO4 / |
#4: 糖 | ChemComp-NDG / |
#5: 水 | ChemComp-HOH / |
非ポリマーの詳細 | N-ACETYL-D-GLUCOSAMINE (NAG): N-ACETYL-D-GLUCOSAMINE IS COVALENTLY ATTACHED TO THE HYDROXYL GROUP ...N-ACETYL-D-GLUCOSAMIN |
-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: 2.93 Å3/Da / 溶媒含有率: 58.07 % / 解説: NONE |
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結晶化 | 温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 詳細: 0.1 M SODIUM ACETATE, PH 5 AND 1.5 M AMMONIUM SULFATE; SITTING-DROP VAPOR-DIFFUSION AT 293.15 K |
-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 MICROMAX-007 HF / 波長: 1.54 |
検出器 | タイプ: RIGAKU CCD / 検出器: CCD / 日付: 2014年2月21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: 1.54 Å / 相対比: 1 |
反射 | 解像度: 2→50 Å / Num. obs: 31941 / % possible obs: 100 % / Observed criterion σ(I): 2 / 冗長度: 5.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.3 |
反射 シェル | 解像度: 2→2.07 Å / 冗長度: 5.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.5 / % possible all: 100 |
-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 ENTRY 1DPF 解像度: 2→91.39 Å / SU B: 2.912 / SU ML: 0.084 / 交差検証法: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.134 / 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 mean: 19.808 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2→91.39 Å
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拘束条件 |
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