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基本情報
登録情報 | データベース: PDB / ID: 1mvc | ||||||
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タイトル | Crystal structure of the human RXR alpha ligand binding domain bound to the synthetic agonist compound BMS 649 and a coactivator peptide | ||||||
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![]() | TRANSCRIPTION / Nuclear Receptor / Retinoic Acid / Agonist recognition / Transcription Factor | ||||||
機能・相同性 | ![]() DNA binding domain binding / positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / LBD domain binding / Carnitine metabolism ...DNA binding domain binding / positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / LBD domain binding / Carnitine metabolism / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of cholesterol efflux / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / retinoic acid receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / locomotor rhythm / aryl hydrocarbon receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of adipose tissue development / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / response to retinoic acid / Recycling of bile acids and salts / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / transcription coregulator binding / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / response to progesterone / nuclear receptor binding / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / circadian regulation of gene expression / Heme signaling / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / Circadian Clock / double-stranded DNA binding / HATs acetylate histones / transcription regulator complex / sequence-specific DNA binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / receptor complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA-binding transcription factor activity / chromatin binding / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Egea, P.F. / Mitschler, A. / Moras, D. | ||||||
![]() | ![]() タイトル: Molecular Recognition of Agonist Ligands by RXRs 著者: Egea, P.F. / Mitschler, A. / Moras, D. | ||||||
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 | ![]() | 62.3 KB | 表示 | ![]() |
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PDB形式 | ![]() | 44.7 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-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 | Although the asymmetric unit contains one monomer of the RXR-peptide-BMS649 complex, The biological assembly is an homodimer generated by the crystallographic two fold axis |
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要素
#1: タンパク質 | 分子量: 26856.039 Da / 分子数: 1 / 断片: ligand binding domain(residues 223-462) / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#2: タンパク質・ペプチド | 分子量: 1579.866 Da / 分子数: 1 / 断片: NR box / 由来タイプ: 合成 詳細: the GRIP1 NR1 coactivator peptide has been synthetized by automatic chemical synthesis 参照: UniProt: Q15596 |
#3: 化合物 | ChemComp-BM6 / |
#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: 2.04 Å3/Da / 溶媒含有率: 47 % | ||||||||||||||||||||||||
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 詳細: PEG 4000, NaCl, Glycerol, BisTris, Pipes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ | ||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 93 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD |
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 | 相対比: 1 |
反射 | 解像度: 1.9→30 Å / Num. all: 82137 / Num. obs: 81070 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / 冗長度: 4.2 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.076 / Net I/σ(I): 18.4 |
反射 シェル | 解像度: 1.9→2 Å / 冗長度: 4 % / Mean I/σ(I) obs: 9.3 / Num. unique all: 1717 / Rsym value: 0.093 / % possible all: 93.5 |
反射 | *PLUS 最低解像度: 30 Å / Num. obs: 19091 / Num. measured all: 81070 / Rmerge(I) obs: 0.076 |
反射 シェル | *PLUS 最低解像度: 2 Å / % possible obs: 93.5 % / Rmerge(I) obs: 0.093 |
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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 id 1FBY 解像度: 1.9→30 Å / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / σ(F): 2 / σ(I): 2 / 立体化学のターゲット値: Engh & Huber
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原子変位パラメータ | Biso mean: 26 Å2 | |||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.9→30 Å
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精密化 | *PLUS 最低解像度: 30 Å / Num. reflection obs: 17234 / % reflection Rfree: 7.5 % / Rfactor all: 0.228 / Rfactor obs: 0.201 / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.201 | |||||||||||||||||||||||||
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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