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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: 3g8u | ||||||
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タイトル | DNA binding domain:GilZ 16bp complex-5 | ||||||
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![]() | TRANSCRIPTION/DNA / glucocorticoid / DNA-binding / allostery / lever arm / transcription / hormone / Alternative initiation / Chromatin regulator / Cytoplasm / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Receptor / Steroid-binding / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger / TRANSCRIPTION-DNA COMPLEX | ||||||
機能・相同性 | ![]() muscle atrophy / negative regulation of synaptic plasticity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of glucocorticoid receptor signaling pathway / response to inactivity / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / positive regulation of cell growth involved in cardiac muscle cell development / SUMOylation of intracellular receptors ...muscle atrophy / negative regulation of synaptic plasticity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of glucocorticoid receptor signaling pathway / response to inactivity / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / positive regulation of cell growth involved in cardiac muscle cell development / SUMOylation of intracellular receptors / response to mercury ion / Nuclear Receptor transcription pathway / steroid hormone binding / nucleus localization / neuroinflammatory response / glucocorticoid metabolic process / hormone binding / microglia differentiation / mammary gland duct morphogenesis / maternal behavior / cellular response to magnesium ion / response to arsenic-containing substance / astrocyte differentiation / negative regulation of vascular permeability / positive regulation of glutamate secretion / cellular response to glucocorticoid stimulus / motor behavior / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / response to corticosterone / positive regulation of dendritic spine development / response to dexamethasone / androgen metabolic process / regulation of glucose metabolic process / postsynaptic density, intracellular component / estrogen response element binding / response to electrical stimulus / nuclear receptor-mediated steroid hormone signaling pathway / core promoter sequence-specific DNA binding / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / Hsp70 protein binding / heat shock protein binding / TBP-class protein binding / steroid binding / cellular response to dexamethasone stimulus / response to activity / synaptic transmission, glutamatergic / female pregnancy / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / lung development / response to insulin / receptor tyrosine kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / response to calcium ion / spindle / circadian rhythm / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / regulation of cell population proliferation / gene expression / double-stranded DNA binding / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / dendritic spine / transcription coactivator activity / nuclear speck / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / centrosome / glutamatergic synapse / chromatin binding / protein-containing complex binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Pufall, M.A. / Yamamoto, K.R. / Meijsing, S.H. | ||||||
![]() | ![]() タイトル: DNA binding site sequence directs glucocorticoid receptor structure and activity. 著者: Meijsing, S.H. / Pufall, M.A. / So, A.Y. / Bates, D.L. / Chen, L. / Yamamoto, K.R. | ||||||
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 | ![]() | 116.2 KB | 表示 | ![]() |
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PDB形式 | ![]() | 87 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 | ![]() | 443.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 457.3 KB | 表示 | |
XML形式データ | ![]() | 12.2 KB | 表示 | |
CIF形式データ | ![]() | 16 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 | ![]() 3fylC ![]() 3g6pC ![]() 3g6qC ![]() 3g6rC ![]() 3g6tC ![]() 3g6uC ![]() 3g8xC ![]() 3g97C ![]() 3g99C ![]() 3g9iC ![]() 3g9jC ![]() 3g9mC ![]() 3g9oC ![]() 3g9pC ![]() 1gluS C: 同じ文献を引用 ( S: 精密化の開始モデル |
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類似構造データ |
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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: 9962.758 Da / 分子数: 2 / 断片: UNP residues 440-525 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() #2: DNA鎖 | | 分子量: 4873.178 Da / 分子数: 1 / 由来タイプ: 合成 詳細: glucocorticoid receptor binding site GilZ bottom strand #3: DNA鎖 | | 分子量: 4922.216 Da / 分子数: 1 / 由来タイプ: 合成 詳細: glucocorticoid receptor binding site GilZ top strand #4: 化合物 | ChemComp-ZN / #5: 水 | ChemComp-HOH / | |
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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: 3.12 Å3/Da / 溶媒含有率: 60.57 % | ||||||||||||||||||||||||||||||||
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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: 5.6 詳細: 50mM MES, pH 5.6, 200mM KCl, 10mM MgCl2, 5% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||
溶液の組成 |
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-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: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2006年9月16日 |
放射 | モノクロメーター: Double flat crystal, 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: 1.115878 Å / 相対比: 1 |
反射 | 解像度: 1.9→30 Å / Num. obs: 27207 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / 冗長度: 6.4 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.068 / Net I/σ(I): 13.4 |
反射 シェル | 解像度: 1.9→1.97 Å / 冗長度: 2.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1647 / Rsym value: 0.624 / % possible all: 56.7 |
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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: 1GLU 解像度: 1.9→29.199 Å / SU ML: 1.3 / σ(F): 0.08 / 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: 82.456 Å2 / ksol: 0.385 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 82.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.9→29.199 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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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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