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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: 1r0o | ||||||
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タイトル | Crystal Structure of the Heterodimeric Ecdysone Receptor DNA-binding Complex | ||||||
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![]() | Transcription/DNA / Ecdsyone receptor / Ultraspiracle / Nuclear receptor / DNA binding domain / Transcription-DNA COMPLEX | ||||||
機能・相同性 | ![]() ecdysone biosynthetic process / repressor ecdysone receptor complex / ecdysis, chitin-based cuticle / larval wandering behavior / regulation of Malpighian tubule diameter / cellular response to ecdysone / regulation of neuron remodeling / Regulation of pyruvate dehydrogenase (PDH) complex / Transcriptional regulation of white adipocyte differentiation / Regulation of lipid metabolism by PPARalpha ...ecdysone biosynthetic process / repressor ecdysone receptor complex / ecdysis, chitin-based cuticle / larval wandering behavior / regulation of Malpighian tubule diameter / cellular response to ecdysone / regulation of neuron remodeling / Regulation of pyruvate dehydrogenase (PDH) complex / Transcriptional regulation of white adipocyte differentiation / Regulation of lipid metabolism by PPARalpha / Signaling by Retinoic Acid / Transcriptional regulation of granulopoiesis / Cytoprotection by HMOX1 / compound eye photoreceptor fate commitment / larval development / ecdysone receptor holocomplex / activator ecdysone receptor complex / dorsal vessel heart proper cell fate commitment / hatching / regulation of hemocyte proliferation / Recycling of bile acids and salts / Carnitine metabolism / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / histoblast morphogenesis / chitin-based cuticle development / SUMOylation of intracellular receptors / chitin-based embryonic cuticle biosynthetic process / Nuclear Receptor transcription pathway / response to ecdysone / Malpighian tubule morphogenesis / larval central nervous system remodeling / VLDLR internalisation and degradation / head involution / ecdysone binding / germ-band shortening / pupariation / ecdysone receptor signaling pathway / cardioblast differentiation / regulation of development, heterochronic / positive regulation of neuron remodeling / mushroom body development / metamorphosis / border follicle cell migration / sperm individualization / imaginal disc-derived wing morphogenesis / autophagic cell death / positive regulation of circadian sleep/wake cycle, sleep / polytene chromosome / hormone binding / peripheral nervous system development / regulation of organ growth / regulation of cellular respiration / cardiac muscle tissue development / bile acid signaling pathway / dendrite morphogenesis / nuclear steroid receptor activity / neuron remodeling / phagocytosis, engulfment / oogenesis / response to starvation / germ cell development / negative regulation of cell differentiation / epidermis development / long-term memory / core promoter sequence-specific DNA binding / steroid binding / transcription corepressor binding / response to cocaine / regulation of autophagy / cholesterol homeostasis / determination of adult lifespan / RNA polymerase II transcription regulatory region sequence-specific DNA binding / autophagy / transcription coactivator binding / negative regulation of inflammatory response / nuclear receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / cell differentiation / transcription cis-regulatory region binding / cell adhesion / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / signaling receptor binding / negative regulation of DNA-templated transcription / lipid binding / dendrite / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Devarakonda, S. / Harp, J.M. / Kim, Y. / Ozyhar, A. / Rastinejad, F. | ||||||
![]() | ![]() タイトル: Structure of the Heterodimeric Ecdysone Receptor DNA-binding Complex 著者: Devarakonda, S. / Harp, J.M. / Kim, Y. / Ozyhar, A. / Rastinejad, F. | ||||||
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 | ![]() | 74.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 51.1 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 | ![]() | 452.4 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 459.8 KB | 表示 | |
XML形式データ | ![]() | 13.9 KB | 表示 | |
CIF形式データ | ![]() | 20.3 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 biological assembly is the macromolecular complex in the asymmetric unit and consists of two DNA binding domains (EcR and USP), bound to an ecdysone response element (IR-1) |
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要素
-Ecdysone Response ... , 2種, 2分子 CD
#1: DNA鎖 | 分子量: 5501.567 Da / 分子数: 1 / 由来タイプ: 合成 |
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#2: DNA鎖 | 分子量: 5492.553 Da / 分子数: 1 / 由来タイプ: 合成 |
-タンパク質 , 2種, 2分子 AB
#3: タンパク質 | 分子量: 10093.663 Da / 分子数: 1 / Fragment: Ultraspiracle DNA binding domain / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: USP / プラスミド: pGEX-2T / 生物種 (発現宿主): Escherichia coli / 発現宿主: ![]() ![]() |
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#4: タンパク質 | 分子量: 12554.819 Da / 分子数: 1 / Fragment: Ecdsyone Receptor DNA binding domain / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: ECR / プラスミド: pGEX-2T / 生物種 (発現宿主): Escherichia coli / 発現宿主: ![]() ![]() |
-非ポリマー , 2種, 283分子 ![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: 化合物 | ChemComp-ZN / #6: 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: 2.51 Å3/Da / 溶媒含有率: 51.09 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 282 K / 手法: 蒸気拡散法 / pH: 5.6 詳細: PEG 3350, Sodium Chloride, DTT, Magnesium Chloride, MES, pH 5.6, VAPOR DIFFUSION, temperature 282K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 |
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結晶化 | *PLUS 温度: 8 ℃ / pH: 7.5 / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: Zhao, Q., (2000) J.Mol.Biol., 296, 509. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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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 4 / 検出器: CCD / 日付: 2002年7月1日 / 詳細: Mirrors |
放射 | モノクロメーター: double crystal / 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: 1.2834 Å / 相対比: 1 |
反射 | 解像度: 2.24→30 Å / Num. all: 17165 / Num. obs: 17114 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 7.5 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 22 |
反射 シェル | 解像度: 2.24→2.34 Å / 冗長度: 7.5 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1540 / Rsym value: 0.456 / % possible all: 97.8 |
反射 | *PLUS 最低解像度: 30 Å / Num. obs: 15928 / % possible obs: 99.6 % |
反射 シェル | *PLUS % possible obs: 97.8 % |
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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: 1R0N 解像度: 2.24→24.77 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 945327.47 / Data cutoff high rms absF: 945327.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 1 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber / 詳細: BULK SOLVENT MODEL USED
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 47.9446 Å2 / ksol: 0.346294 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 45.5 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: 2.24→24.77 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.24→2.38 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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精密化 | *PLUS 最低解像度: 20 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||
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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