+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3431 | |||||||||
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タイトル | Negative Stain EM of NuRD subcomplex of RBBP4 and MTA1 (Human). | |||||||||
マップデータ | Human MTA1 truncation mutant (residues 449 to 715) bound to two copies of RBBP4. | |||||||||
試料 |
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キーワード | NuRD complex / RBBP4 / MTA1 / transcription regulation / chromatin / protein structure | |||||||||
機能・相同性 | 機能・相同性情報 CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Transcription of E2F targets under negative control by DREAM complex ...CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Transcription of E2F targets under negative control by DREAM complex / positive regulation of protein autoubiquitination / Polo-like kinase mediated events / response to ionizing radiation / negative regulation of gene expression, epigenetic / positive regulation of stem cell population maintenance / ATPase complex / G1/S-Specific Transcription / entrainment of circadian clock by photoperiod / Sin3-type complex / locomotor rhythm / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / SUMOylation of transcription factors / histone deacetylase complex / G0 and Early G1 / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / negative regulation of cell migration / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / brain development / PKMTs methylate histone lysines / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / transcription corepressor activity / double-strand break repair / nucleosome assembly / nuclear envelope / histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / RNA polymerase II-specific DNA-binding transcription factor binding / microtubule / DNA replication / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / ネガティブ染色法 / 解像度: 29.7 Å | |||||||||
データ登録者 | Schmidberger JW / Sharif Tabar M / Torrado M / Silva APG / Landsberg MJ / Brilault L / Alqarni S / Zeng YC / Parker BL / Low JKK / Mackay JP | |||||||||
引用 | ジャーナル: Protein Sci / 年: 2016 タイトル: The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7. 著者: Jason W Schmidberger / Mehdi Sharifi Tabar / Mario Torrado / Ana P G Silva / Michael J Landsberg / Lou Brillault / Saad AlQarni / Yi Cheng Zeng / Benjamin L Parker / Jason K K Low / Joel P Mackay / 要旨: The nucleosome remodeling and deacetylase (NuRD) complex remodels the genome in the context of both gene transcription and DNA damage repair. It is essential for normal development and is distributed ...The nucleosome remodeling and deacetylase (NuRD) complex remodels the genome in the context of both gene transcription and DNA damage repair. It is essential for normal development and is distributed across multiple tissues in organisms ranging from mammals to nematode worms. In common with other chromatin-remodeling complexes, however, its molecular mechanism of action is not well understood and only limited structural information is available to show how the complex is assembled. As a step towards understanding the structure of the NuRD complex, we have characterized the interaction between two subunits: the metastasis associated protein MTA1 and the histone-binding protein RBBP4. We show that MTA1 can bind to two molecules of RBBP4 and present negative stain electron microscopy and chemical crosslinking data that allow us to build a low-resolution model of an MTA1-(RBBP4)2 subcomplex. These data build on our understanding of NuRD complex structure and move us closer towards an understanding of the biochemical basis for the activity of this complex. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_3431.map.gz | 402.7 KB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3431-v30.xml emd-3431.xml | 11.8 KB 11.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_3431_fsc.xml | 2.3 KB | 表示 | FSCデータファイル |
画像 | emd_3431.tif | 295.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3431 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3431 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_3431_validation.pdf.gz | 227.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_3431_full_validation.pdf.gz | 226.8 KB | 表示 | |
XML形式データ | emd_3431_validation.xml.gz | 6.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3431 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3431 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_3431.map.gz / 形式: CCP4 / 大きさ: 538.1 KB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Human MTA1 truncation mutant (residues 449 to 715) bound to two copies of RBBP4. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 5.58 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : Human MTA1 C-terminal truncation mutant (residues 449 to 715) bou...
全体 | 名称: Human MTA1 C-terminal truncation mutant (residues 449 to 715) bound to two copies of RBBP4. |
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要素 |
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-超分子 #1000: Human MTA1 C-terminal truncation mutant (residues 449 to 715) bou...
超分子 | 名称: Human MTA1 C-terminal truncation mutant (residues 449 to 715) bound to two copies of RBBP4. タイプ: sample / ID: 1000 集合状態: One copy of MTA1-C binds to two copies of RBBP4. Number unique components: 2 |
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分子量 | 実験値: 130 KDa / 理論値: 128 KDa / 手法: SDS PAGE |
-分子 #1: Metastasis-associated protein MTA1 C-terminus (449-715)
分子 | 名称: Metastasis-associated protein MTA1 C-terminus (449-715) タイプ: protein_or_peptide / ID: 1 / Name.synonym: MTA (449-715) / コピー数: 1 / 集合状態: 1 X MTA1, 2 X RBBP4 / 組換発現: Yes |
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由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human |
分子量 | 実験値: 30 KDa / 理論値: 30 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) / 組換細胞: HEK293 / 組換プラスミド: pcDNA3.1 |
配列 | UniProtKB: Metastasis-associated protein MTA1 |
-分子 #2: Histone-binding protein RBBP4
分子 | 名称: Histone-binding protein RBBP4 / タイプ: protein_or_peptide / ID: 2 / Name.synonym: RBBP4 / コピー数: 2 / 組換発現: Yes |
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由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human |
分子量 | 実験値: 50 KDa / 理論値: 48 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) / 組換細胞: HEK293 / 組換プラスミド: pcDNA3.1 |
配列 | UniProtKB: Histone-binding protein RBBP4 |
-実験情報
-構造解析
手法 | ネガティブ染色法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.01 mg/mL |
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緩衝液 | pH: 8.2 / 詳細: 50 mM HEPES KOH pH 8.2, 150 mM NaCl, 1 mM DTT. |
染色 | タイプ: NEGATIVE 詳細: After an incubation time of 5 min, the grid was blotted and washed with five drops of distilled water, blotted again and subsequently stained with a 2% (w/v) uranyl acetate solution for one ...詳細: After an incubation time of 5 min, the grid was blotted and washed with five drops of distilled water, blotted again and subsequently stained with a 2% (w/v) uranyl acetate solution for one minute. Excess stain was then blotted away and the grid allowed to dry under air at ambient conditions. |
グリッド | 詳細: Glow-discharged, carbon-coated 400-mesh copper grid (GSCu400CC ProSciTech) |
凍結 | 凍結剤: NONE / 装置: OTHER |
-電子顕微鏡法
顕微鏡 | FEI TECNAI 12 |
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日付 | 2015年12月17日 |
撮影 | カテゴリ: CCD / フィルム・検出器のモデル: OTHER / 実像数: 400 |
電子線 | 加速電圧: 120 kV / 電子線源: LAB6 |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 54000 |
試料ステージ | 試料ホルダーモデル: PHILIPS ROTATION HOLDER |
-画像解析
-原子モデル構築 1
初期モデル | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D |
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ソフトウェア | 名称: Chimera |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |