+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4k4j | ||||||
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タイトル | Crystal structure of human Retinoid X Receptor alpha-ligand binding domain complex with 9cUAB30 and the coactivator peptide GRIP-1 | ||||||
要素 |
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キーワード | TRANSCRIPTION / ligand binding domain / cancer / 9-cis-UAB30 | ||||||
機能・相同性 | 機能・相同性情報 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 / Carnitine shuttle / TGFBR3 expression / retinoic acid 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 / Carnitine shuttle / TGFBR3 expression / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / nuclear steroid receptor activity / 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 / 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 cholesterol efflux / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / retinoic acid receptor signaling pathway / positive regulation of bone mineralization / response to retinoic acid / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to hormone stimulus / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / transcription coregulator binding / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / HATs acetylate histones / double-stranded DNA binding / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / cell differentiation / receptor complex / nuclear body / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 2 Å | ||||||
データ登録者 | Xia, G. / Smith, C.D. / Muccio, D.D. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 2014 タイトル: Defining the Communication between Agonist and Coactivator Binding in the Retinoid X Receptor alpha Ligand Binding Domain. 著者: Boerma, L.J. / Xia, G. / Qui, C. / Cox, B.D. / Chalmers, M.J. / Smith, C.D. / Lobo-Ruppert, S. / Griffin, P.R. / Muccio, D.D. / Renfrow, M.B. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 4k4j.cif.gz | 61.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4k4j.ent.gz | 43.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4k4j.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 4k4j_validation.pdf.gz | 694.7 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4k4j_full_validation.pdf.gz | 699.7 KB | 表示 | |
XML形式データ | 4k4j_validation.xml.gz | 12.4 KB | 表示 | |
CIF形式データ | 4k4j_validation.cif.gz | 17 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/k4/4k4j ftp://data.pdbj.org/pub/pdb/validation_reports/k4/4k4j | HTTPS FTP |
-関連構造データ
関連構造データ | 4k6iC 3oapS S: 精密化の開始モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 25897.021 Da / 分子数: 1 / 断片: ligand binding domain, UNP residues 228-458 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 株: P19793 / 遺伝子: NR2B1, RXRA, RXRA NR2B1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P19793 |
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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: coactivator peptide, UNP residues 686-698 / 由来タイプ: 合成 / 詳細: GRIP-1 from AnaSpec Inc / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q15596 |
#3: 化合物 | ChemComp-1O8 / ( |
#4: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.21 Å3/Da / 溶媒含有率: 44.23 % |
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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: 5-10% PEG4000, 2-5% Glycerol, 0.1M Bis-Tris, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-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: 回転陽極 / タイプ: OTHER / 波長: 1.315 Å |
検出器 | タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2004年8月2日 |
放射 | モノクロメーター: Graphite / 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: 1.315 Å / 相対比: 1 |
反射 | 解像度: 2→29.53 Å / Num. all: 94263 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / 冗長度: 5.45 % / Rmerge(I) obs: 0.048 / Rsym value: 0.322 / Net I/σ(I): 17.3 |
反射 シェル | 解像度: 2→2.07 Å / 冗長度: 4.47 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 1616 / Rsym value: 0.322 / % possible all: 99.1 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 3OAP 解像度: 2→29.53 Å / σ(F): 2 / σ(I): 2 / 立体化学のターゲット値: Engh & Huber
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精密化ステップ | サイクル: LAST / 解像度: 2→29.53 Å
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拘束条件 |
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