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基本情報
登録情報 | データベース: PDB / ID: 3h82 | ||||||
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タイトル | Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains with the artificial ligand THS020 | ||||||
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![]() | TRANSCRIPTION / PAS domain / heterodimer / protein ligand complex. / Activator / Angiogenesis / Congenital erythrocytosis / Developmental protein / Differentiation / Disease mutation / DNA-binding / Hydroxylation / Nucleus / Phosphoprotein / Transcription regulation / Ubl conjugation / Alternative splicing / Polymorphism | ||||||
機能・相同性 | ![]() myoblast fate commitment / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / Cellular response to hypoxia / aryl hydrocarbon receptor complex / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / positive regulation of protein sumoylation ...myoblast fate commitment / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / Cellular response to hypoxia / aryl hydrocarbon receptor complex / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / positive regulation of protein sumoylation / norepinephrine metabolic process / Xenobiotics / surfactant homeostasis / Phase I - Functionalization of compounds / positive regulation of vascular endothelial growth factor receptor signaling pathway / epithelial cell maturation / Regulation of gene expression by Hypoxia-inducible Factor / aryl hydrocarbon receptor binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / blood vessel remodeling / Endogenous sterols / cis-regulatory region sequence-specific DNA binding / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / visual perception / Pexophagy / positive regulation of glycolytic process / regulation of heart rate / mitochondrion organization / erythrocyte differentiation / positive regulation of erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / mRNA transcription by RNA polymerase II / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / PPARA activates gene expression / transcription coactivator binding / multicellular organismal-level iron ion homeostasis / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Neddylation / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / transcription regulator complex / sequence-specific DNA binding / cell differentiation / nuclear body / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Key, J.M. / Scheuermann, T.H. / Anderson, P.C. / Daggett, V. / Gardner, K.H. | ||||||
![]() | ![]() タイトル: Principles of ligand binding within a completely buried cavity in HIF2alpha PAS-B 著者: Key, J. / Scheuermann, T.H. / Anderson, P.C. / Daggett, V. / Gardner, K.H. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 70.3 KB | 表示 | ![]() |
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PDB形式 | ![]() | 50.8 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 779.7 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 785 KB | 表示 | |
XML形式データ | ![]() | 14.6 KB | 表示 | |
CIF形式データ | ![]() | 20.5 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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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詳細 | The biologically relevant complex is present in the ASU |
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要素
#1: タンパク質 | 分子量: 14243.098 Da / 分子数: 1 断片: ARNT C-terminal PAS domain (UNP residues 356 to 470) 変異: E362R / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 遺伝子: ARNT, Aryl Hydrocarbon Receptor Nuclear Translocator, BHLHE2 プラスミド: phis-GB1-ARNT-PAS-B / 発現宿主: ![]() ![]() |
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#2: タンパク質 | 分子量: 13538.300 Da / 分子数: 1 断片: HIF2alpha C-terminal PAS domain (UNP residues 239 to 350) 変異: R247E / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 遺伝子: EPAS1, HIF2A, Hypoxia Inducible Factor 2 alpha, MOP2 プラスミド: phis-GB1-HIF2aPAS-B / 発現宿主: ![]() ![]() |
#3: 化合物 | ChemComp-020 / |
#4: 水 | ChemComp-HOH / |
-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: 2.07 Å3/Da / 溶媒含有率: 40.72 % |
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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: 0.1M BisTris, 25% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: SBC-2 / 検出器: CCD / 日付: 2007年12月14日 |
放射 | モノクロメーター: custom / 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: 0.97915 Å / 相対比: 1 |
反射 | 解像度: 1.5→40 Å / Num. all: 34380 / Num. obs: 34380 / % possible obs: 94.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / 冗長度: 3 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 21.8 |
反射 シェル | 解像度: 1.5→1.53 Å / 冗長度: 1.7 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.48 / Num. unique all: 1241 / % possible all: 68.8 |
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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: PDB entry 3F1N 解像度: 1.5→26.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.686 / SU ML: 0.064 / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.1815 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.5→26.44 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.5→1.53 Å / Total num. of bins used: 20
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