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基本情報
登録情報 | データベース: PDB / ID: 1mzn | ||||||
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タイトル | CRYSTAL STRUCTURE at 1.9 ANGSTROEMS RESOLUTION OF THE HOMODIMER OF 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 Receptors / Agonist | ||||||
機能・相同性 | ![]() retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway ...retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / locomotor rhythm / aryl hydrocarbon receptor binding / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / positive regulation of bone mineralization / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / Recycling of bile acids and salts / transcription regulator inhibitor activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / hormone-mediated signaling pathway / positive regulation of adipose tissue development / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / peptide binding / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear receptor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nuclear receptor activity / : / sequence-specific double-stranded DNA binding / nervous system development / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / receptor complex / transcription cis-regulatory region binding / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / positive 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 / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() synthetic construct (人工物) | ||||||
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. #1: ![]() タイトル: Crystal structure of the human RXRalpha ligand-binding domain bound to its natural ligand: 9-cis retinoic acid 著者: Egea, P.F. / Mitschler, A. / Rochel, N. / Ruff, M. / Chambon, P. / 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 | ![]() | 214.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 167.5 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 | ![]() | 654.5 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 666.3 KB | 表示 | |
XML形式データ | ![]() | 20.6 KB | 表示 | |
CIF形式データ | ![]() | 34.2 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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要素
#1: タンパク質 | 分子量: 26856.039 Da / 分子数: 4 / 断片: ligand binding domain(residues 223-462) / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質・ペプチド | 分子量: 1579.866 Da / 分子数: 4 / 断片: NR box / 由来タイプ: 合成 詳細: CHEMICAL SYNTHESIS, This is the synthetic peptide fragment from GRIP-1 coactivator 由来: (合成) synthetic construct (人工物) / 参照: UniProt: Q15596 #3: 化合物 | ChemComp-BM6 / #4: 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: 2.38 Å3/Da / 溶媒含有率: 45 % | ||||||||||||||||||||||||
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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, Pipes, BisTris, glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / pH: 7 | ||||||||||||||||||||||||
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 | 波長: 0.9 Å / 相対比: 1 |
反射 | 解像度: 1.9→30 Å / Num. all: 194870 / Num. obs: 191828 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / 冗長度: 2.4 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 15.6 |
反射 シェル | 解像度: 1.9→2 Å / 冗長度: 2.4 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 7.9 / Num. unique all: 6983 / Rsym value: 0.124 / % possible all: 96.6 |
反射 | *PLUS 最高解像度: 2 Å / 最低解像度: 30 Å / Num. obs: 79918 / % possible obs: 95.9 % / Num. measured all: 194870 / Rmerge(I) obs: 0.063 |
反射 シェル | *PLUS 最高解像度: 2 Å / 最低解像度: 2.1 Å / % possible obs: 96.6 % / Rmerge(I) obs: 0.124 |
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解析
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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: 25 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 最高解像度: 2 Å / 最低解像度: 30 Å / Num. reflection obs: 71161 / Rfactor all: 0.232 / Rfactor obs: 0.195 / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.195 | |||||||||||||||||||||||||
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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