+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5zoo | ||||||
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タイトル | Crystal structure of histone deacetylase 4 (HDAC4) in complex with a SMRT corepressor SP1 fragment | ||||||
要素 |
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キーワード | HYDROLASE (加水分解酵素) / protein-peptide complex | ||||||
機能・相同性 | 機能・相同性情報 RUNX2 regulates chondrocyte maturation / Loss of MECP2 binding ability to the NCoR/SMRT complex / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / positive regulation of protein sumoylation / regulation of protein binding ...RUNX2 regulates chondrocyte maturation / Loss of MECP2 binding ability to the NCoR/SMRT complex / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / positive regulation of protein sumoylation / regulation of protein binding / negative regulation of transcription by competitive promoter binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / ヒストン脱アセチル化酵素 / protein lysine deacetylase activity / Notch binding / negative regulation of glycolytic process / SUMO transferase activity / histone deacetylase activity / negative regulation of gene expression, epigenetic / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / type I interferon-mediated signaling pathway / B cell activation / Notch-HLH transcription pathway / potassium ion binding / histone deacetylase complex / protein sumoylation / RUNX3 regulates p14-ARF / Regulation of MECP2 expression and activity / estrous cycle / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to organonitrogen compound / transcription repressor complex / 授乳 / Regulation of lipid metabolism by PPARalpha / cerebellum development / response to interleukin-1 / SUMOylation of chromatin organization proteins / B cell differentiation / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / Nuclear Receptor transcription pathway / histone deacetylase binding / transcription corepressor activity / positive regulation of DNA-binding transcription factor activity / response to estradiol / nervous system development / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / molecular adaptor activity / nuclear body / nuclear speck / クロマチンリモデリング / 炎症 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / クロマチン / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / 核質 / 生体膜 / identical protein binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.85 Å | ||||||
データ登録者 | Park, S.Y. / Hwang, H.J. / Kim, J.S. | ||||||
資金援助 | 韓国, 1件
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引用 | ジャーナル: Nucleic Acids Res. / 年: 2018 タイトル: Structural basis of the specific interaction of SMRT corepressor with histone deacetylase 4. 著者: Park, S.Y. / Kim, G.S. / Hwang, H.J. / Nam, T.H. / Park, H.S. / Song, J. / Jang, T.H. / Lee, Y.C. / Kim, J.S. | ||||||
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 | 5zoo.cif.gz | 179.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5zoo.ent.gz | 139.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5zoo.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/zo/5zoo ftp://data.pdbj.org/pub/pdb/validation_reports/zo/5zoo | HTTPS FTP |
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-関連構造データ
-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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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 43399.152 Da / 分子数: 1 / 断片: UNP residues 652-1052 / 変異: H976Y / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HDAC4, KIAA0288 / プラスミド: pET21a / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) 参照: UniProt: P56524, ヒストン脱アセチル化酵素 | ||||||
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#2: タンパク質・ペプチド | 分子量: 1587.803 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9Y618*PLUS | ||||||
#3: 化合物 | #4: 化合物 | #5: 水 | ChemComp-HOH / | 配列の詳細 | The alanine (chain G, 1) is remaining amino acid after TEV digestion to remove expression tag. | |
-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: 3.92 Å3/Da / 溶媒含有率: 68.63 % |
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結晶化 | 温度: 295 K / 手法: 蒸発脱水法 / pH: 7.5 / 詳細: PEG 3350, iso-propanol |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: シンクロトロン / サイト: PAL/PLS / ビームライン: 5C (4A) / 波長: 1 Å |
検出器 | タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2013年5月5日 |
放射 | モノクロメーター: Si(111) / 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 Å / 相対比: 1 |
反射 | 解像度: 1.846→29.565 Å / Num. obs: 57039 / % possible obs: 98.4 % / 冗長度: 3.2 % / Biso Wilson estimate: 24.19 Å2 / Rsym value: 0.138 / Net I/σ(I): 12 |
反射 シェル | 解像度: 1.85→1.88 Å / Rsym value: 0.45 |
-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: 2VQW 解像度: 1.85→9.989 Å / SU ML: 0.15 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 16.59 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.85→9.989 Å
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拘束条件 |
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精密化 TLS | 手法: refined / Origin x: 56.4793 Å / Origin y: -17.636 Å / Origin z: 2.1535 Å
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精密化 TLSグループ | Selection details: all |