+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3tvd | ||||||
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タイトル | Crystal Structure of Mouse RhoA-GTP complex | ||||||
要素 | Transforming protein RhoA | ||||||
キーワード | SIGNALING PROTEIN / Alpha helical (Αヘリックス) / Protein_GTP complex / Helical protein / GTP binding protein / Regulates signal transduction pathway / GTP / Nil / Membrane (生体膜) | ||||||
機能・相同性 | 機能・相同性情報 trabecula morphogenesis / EPHA-mediated growth cone collapse / PCP/CE pathway / RHO GTPases activate PKNs / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / : / Sema4D mediated inhibition of cell attachment and migration / RHO GTPases Activate ROCKs / ERBB2 Regulates Cell Motility ...trabecula morphogenesis / EPHA-mediated growth cone collapse / PCP/CE pathway / RHO GTPases activate PKNs / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / : / Sema4D mediated inhibition of cell attachment and migration / RHO GTPases Activate ROCKs / ERBB2 Regulates Cell Motility / RHO GTPases activate KTN1 / GPVI-mediated activation cascade / PI3K/AKT activation / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Sema4D induced cell migration and growth-cone collapse / Ovarian tumor domain proteases / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / VEGFA-VEGFR2 Pathway / RHO GTPases Activate Formins / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / G alpha (12/13) signalling events / : / RHO GTPases activate CIT / : / regulation of actin polymerization or depolymerization / regulation of dendrite development / response to xenobiotic stimulus => GO:0009410 / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / positive regulation of lipase activity / endothelial tube lumen extension / regulation of modification of synaptic structure / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / cellular response to progesterone stimulus / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / regulation of neural precursor cell proliferation / cleavage furrow formation / EPHB-mediated forward signaling / cortical cytoskeleton organization / regulation of modification of postsynaptic actin cytoskeleton / positive regulation of smooth muscle contraction / 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 / G beta:gamma signalling through PI3Kgamma / beta selection / establishment of epithelial cell apical/basal polarity / negative regulation of cell size / negative regulation of oxidative phosphorylation / apolipoprotein A-I-mediated signaling pathway / GTP metabolic process / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / ossification involved in bone maturation / positive regulation of alpha-beta T cell differentiation / 歯の発生 / Neutrophil degranulation / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / negative chemotaxis / Rho GDP-dissociation inhibitor binding / myosin binding / stress-activated protein kinase signaling cascade / positive regulation of actin filament polymerization / stress fiber assembly / regulation of neuron projection development / androgen receptor signaling pathway / positive regulation of cytokinesis / cerebral cortex cell migration / cellular response to cytokine stimulus / 分裂溝 / regulation of calcium ion transport / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Rho protein signal transduction / positive regulation of cell adhesion / mitotic spindle assembly / negative regulation of neuron differentiation / endothelial cell migration / positive regulation of T cell migration / response to amino acid / response to glucose / regulation of microtubule cytoskeleton organization / response to mechanical stimulus / cytoplasmic microtubule organization / negative regulation of canonical NF-kappaB signal transduction / skeletal muscle tissue development / regulation of cell migration / negative regulation of reactive oxygen species biosynthetic process / response to glucocorticoid / positive regulation of vasoconstriction / positive regulation of stress fiber assembly 類似検索 - 分子機能 | ||||||
生物種 | Rattus norvegicus (ドブネズミ) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 2.989 Å | ||||||
データ登録者 | Swaminathan, K. / Pal, K. / Jobichen, C. | ||||||
引用 | ジャーナル: J.Struct.Funct.Genom. / 年: 2012 タイトル: Crystal structure of mouse RhoA:GTPgammaS complex in a centered lattice. 著者: Jobichen, C. / Pal, K. / Swaminathan, 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 | 3tvd.cif.gz | 86.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3tvd.ent.gz | 64.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3tvd.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/tv/3tvd ftp://data.pdbj.org/pub/pdb/validation_reports/tv/3tvd | HTTPS FTP |
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-関連構造データ
関連構造データ | 1ftnS 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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非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域:
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-要素
#1: タンパク質 | 分子量: 21813.186 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Arha, Arha2, Rhoa / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P61589 #2: 化合物 | #3: 化合物 | #4: 水 | ChemComp-HOH / | |
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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: 2.59 Å3/Da / 溶媒含有率: 52.55 % |
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.6 詳細: 0.2M Ammonium acetate, 0.1M Sodium acetate (pH4.6), 30% Polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: 1.5418 Å |
検出器 | タイプ: RIGAKU SATURN 944+ / 検出器: CCD / 日付: 2011年3月21日 / 詳細: mirrors |
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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2.989→29 Å / Num. all: 8595 / Num. obs: 8595 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / 冗長度: 4.9 % / Rsym value: 0.16 |
反射 シェル | 解像度: 3→3.15 Å / 冗長度: 4.9 % / Rsym value: 0.34 / % possible all: 99 |
-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 1FTN 解像度: 2.989→14.999 Å / SU ML: 0.6 / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 25.32 / 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: 0.83 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 10.69 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ |
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精密化ステップ | サイクル: LAST / 解像度: 2.989→14.999 Å
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拘束条件 |
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Refine LS restraints NCS |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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