+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6g16 | ||||||
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タイトル | Structure of the human RBBP4:MTA1(464-546) complex showing loop exchange | ||||||
要素 |
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キーワード | TRANSCRIPTION (転写 (生物学)) / WD40 / corepressor (コリプレッサー) / metastasis | ||||||
機能・相同性 | 機能・相同性情報 CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / 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 ...CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / 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 / Polo-like kinase mediated events / positive regulation of protein autoubiquitination / negative regulation of gene expression, epigenetic / response to ionizing radiation / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / positive regulation of stem cell population maintenance / entrainment of circadian clock by photoperiod / Transcriptional Regulation by E2F6 / locomotor rhythm / RNA Polymerase I Transcription Initiation / histone deacetylase complex / SUMOylation of transcription factors / G0 and Early G1 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / 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 / brain development / circadian regulation of gene expression / PKMTs methylate histone lysines / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / histone deacetylase binding / transcription corepressor activity / double-strand break repair / 核膜 / histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / 微小管 / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / DNA複製 / chromosome, telomeric region / transcription coactivator activity / クロマチンリモデリング / 細胞周期 / 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 / クロマチン / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / シグナル伝達 / protein-containing complex / 核質 / metal ion 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: 2.8 Å | ||||||
データ登録者 | Millard, C.J. / Varma, N. / Fairall, L. / Schwabe, J.W.R. | ||||||
資金援助 | 英国, 1件
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引用 | ジャーナル: Elife / 年: 2016 タイトル: The structure of the core NuRD repression complex provides insights into its interaction with chromatin. 著者: Christopher J Millard / Niranjan Varma / Almutasem Saleh / Kyle Morris / Peter J Watson / Andrew R Bottrill / Louise Fairall / Corinne J Smith / John W R Schwabe / 要旨: The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure ...The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin. #1: ジャーナル: Elife / 年: 2016 タイトル: The structure of the core NuRD repression complex provides insights into its interaction with chromatin. 著者: Christopher J Millard / Niranjan Varma / Almutasem Saleh / Kyle Morris / Peter J Watson / Andrew R Bottrill / Louise Fairall / Corinne J Smith / John W R Schwabe / 要旨: The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure ...The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin. | ||||||
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 | 6g16.cif.gz | 362.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6g16.ent.gz | 296.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6g16.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/g1/6g16 ftp://data.pdbj.org/pub/pdb/validation_reports/g1/6g16 | 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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単位格子 |
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-要素
#1: タンパク質 | 分子量: 47709.527 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RBBP4, RBAP48 / プラスミド: PCDNA3 / 細胞株 (発現宿主): HEK293F / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q09028 #2: タンパク質 | 分子量: 9773.559 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MTA1 / 細胞株 (発現宿主): HEK293F / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q13330 |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 5 |
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-試料調製
結晶 | マシュー密度: 2.56 Å3/Da / 溶媒含有率: 52.01 % |
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5 詳細: 0.21 M AMMONIUM CITRATE, 19% PEG 3350, 15 mM MALTOSE pH 7.5 |
-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: シンクロトロン / サイト: Diamond / ビームライン: I24 / 波長: 0.96861 Å |
検出器 | タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2017年3月9日 |
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: 0.96861 Å / 相対比: 1 |
反射 | 解像度: 2.8→95.4 Å / Num. obs: 51450 / % possible obs: 95 % / 冗長度: 9.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.5 |
反射 シェル | 解像度: 2.8→2.88 Å / 冗長度: 9.2 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 3.4 / % possible all: 96.9 |
-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: 5FXY 解像度: 2.8→95.33 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.876 / SU B: 17.132 / SU ML: 0.333 / 交差検証法: THROUGHOUT / ESU R Free: 0.407 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 56.404 Å2
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精密化ステップ | サイクル: 1 / 解像度: 2.8→95.33 Å
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拘束条件 |
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