+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11839 | ||||||||||||
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タイトル | Structure of the extended MTA1/HDAC1/MBD2/RBBP4 NURD deacetylase complex | ||||||||||||
マップデータ | Extended NuRD deacetylase complex | ||||||||||||
試料 |
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キーワード | Deacetylase / Complex / TRANSCRIPTION | ||||||||||||
機能・相同性 | 機能・相同性情報 Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / satellite DNA binding / CAF-1 complex / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / ventricular cardiac muscle tissue development ...Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / satellite DNA binding / CAF-1 complex / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / ventricular cardiac muscle tissue development / fungiform papilla formation / negative regulation of androgen receptor signaling pathway / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / endoderm development / DNA replication-dependent chromatin assembly / maternal behavior / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / NuRD complex / DNA methylation-dependent heterochromatin formation / siRNA binding / protein deacetylation / ESC/E(Z) complex / Transcription of E2F targets under negative control by DREAM complex / STAT3 nuclear events downstream of ALK signaling / Polo-like kinase mediated events / positive regulation of protein autoubiquitination / histone deacetylase / C2H2 zinc finger domain binding / methyl-CpG binding / protein lysine deacetylase activity / positive regulation of signaling receptor activity / 加水分解酵素; ペプチド以外のCN結合加水分解酵素; 鎖状アミドに作用 / embryonic digit morphogenesis / negative regulation of gene expression, epigenetic / positive regulation of oligodendrocyte differentiation / histone deacetylase activity / response to ionizing radiation / Sin3-type complex / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / ATPase complex / cellular response to platelet-derived growth factor stimulus / Notch-HLH transcription pathway / eyelid development in camera-type eye / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / E-box binding / entrainment of circadian clock by photoperiod / odontogenesis of dentin-containing tooth / locomotor rhythm / RNA Polymerase I Transcription Initiation / SUMOylation of transcription factors / histone deacetylase complex / hair follicle placode formation / cellular response to organic cyclic compound / Regulation of MECP2 expression and activity / G0 and Early G1 / NF-kappaB binding / positive regulation of Wnt signaling pathway / negative regulation by host of viral transcription / RNA polymerase II core promoter sequence-specific DNA binding / embryonic organ development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / heterochromatin / Nuclear events stimulated by ALK signaling in cancer / Cyclin E associated events during G1/S transition / response to mechanical stimulus / MECP2 regulates neuronal receptors and channels / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / nucleosome binding / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / transcription repressor complex / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / negative regulation of cell migration / response to nutrient levels / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / Deactivation of the beta-catenin transactivating complex / hippocampus development / promoter-specific chromatin binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of smooth muscle cell proliferation / Formation of the beta-catenin:TCF transactivating complex / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 19.4 Å | ||||||||||||
データ登録者 | Millard CJ / Fairall L | ||||||||||||
資金援助 | 英国, 3件
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引用 | ジャーナル: Nucleic Acids Res / 年: 2020 タイトル: The topology of chromatin-binding domains in the NuRD deacetylase complex. 著者: Christopher J Millard / Louise Fairall / Timothy J Ragan / Christos G Savva / John W R Schwabe / 要旨: Class I histone deacetylase complexes play essential roles in many nuclear processes. Whilst they contain a common catalytic subunit, they have diverse modes of action determined by associated ...Class I histone deacetylase complexes play essential roles in many nuclear processes. Whilst they contain a common catalytic subunit, they have diverse modes of action determined by associated factors in the distinct complexes. The deacetylase module from the NuRD complex contains three protein domains that control the recruitment of chromatin to the deacetylase enzyme, HDAC1/2. Using biochemical approaches and cryo-electron microscopy, we have determined how three chromatin-binding domains (MTA1-BAH, MBD2/3 and RBBP4/7) are assembled in relation to the core complex so as to facilitate interaction of the complex with the genome. We observe a striking arrangement of the BAH domains suggesting a potential mechanism for binding to di-nucleosomes. We also find that the WD40 domains from RBBP4 are linked to the core with surprising flexibility that is likely important for chromatin engagement. A single MBD2 protein binds asymmetrically to the dimerisation interface of the complex. This symmetry mismatch explains the stoichiometry of the complex. Finally, our structures suggest how the holo-NuRD might assemble on a di-nucleosome substrate. | ||||||||||||
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_11839.map.gz | 1.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11839-v30.xml emd-11839.xml | 26.7 KB 26.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_11839_fsc.xml | 6.5 KB | 表示 | FSCデータファイル |
画像 | emd_11839.png | 84.5 KB | ||
マスクデータ | emd_11839_msk_1.map | 22.2 MB | マスクマップ | |
Filedesc metadata | emd-11839.cif.gz | 7.8 KB | ||
その他 | emd_11839_half_map_1.map.gz emd_11839_half_map_2.map.gz | 17 MB 17 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11839 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11839 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_11839_validation.pdf.gz | 684.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_11839_full_validation.pdf.gz | 683.9 KB | 表示 | |
XML形式データ | emd_11839_validation.xml.gz | 12.1 KB | 表示 | |
CIF形式データ | emd_11839_validation.cif.gz | 16.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11839 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11839 | 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_11839.map.gz / 形式: CCP4 / 大きさ: 22.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Extended NuRD deacetylase complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.16 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
-マスク #1
ファイル | emd_11839_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Extended NuRD deacetylase complex - half1
ファイル | emd_11839_half_map_1.map | ||||||||||||
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注釈 | Extended NuRD deacetylase complex - half1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Extended NuRD deacetylase complex - half2
ファイル | emd_11839_half_map_2.map | ||||||||||||
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注釈 | Extended NuRD deacetylase complex - half2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Extended NuRD deacetylase complex containing two copies of MTA1, ...
全体 | 名称: Extended NuRD deacetylase complex containing two copies of MTA1, HDAC1 and RBBP4 and a single copy of MBD2 |
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要素 |
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-超分子 #1: Extended NuRD deacetylase complex containing two copies of MTA1, ...
超分子 | 名称: Extended NuRD deacetylase complex containing two copies of MTA1, HDAC1 and RBBP4 and a single copy of MBD2 タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#4 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 340 KDa |
-分子 #1: Methyl-CpG-binding domain protein 2
分子 | 名称: Methyl-CpG-binding domain protein 2 / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 43.323625 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MRAHPGGGRC CPEQEEGESA AGGSGAGGDS AIEQGGQGSA LAPSPVSGVR REGARGGGRG RGRWKQAGRG GGVCGRGRGR GRGRGRGRG RGRGRGRPPS GGSGLGGDGG GCGGGGSGGG GAPRREPVPF PSGSAGPGPR GPRATESGKR MDCPALPPGW K KEEVIRKS ...文字列: MRAHPGGGRC CPEQEEGESA AGGSGAGGDS AIEQGGQGSA LAPSPVSGVR REGARGGGRG RGRWKQAGRG GGVCGRGRGR GRGRGRGRG RGRGRGRPPS GGSGLGGDGG GCGGGGSGGG GAPRREPVPF PSGSAGPGPR GPRATESGKR MDCPALPPGW K KEEVIRKS GLSAGKSDVY YFSPSGKKFR SKPQLARYLG NTVDLSSFDF RTGKMMPSKL QKNKQRLRND PLNQNKGKPD LN TTLPIRQ TASIFKQPVT KVTNHPSNKV KSDPQRMNEQ PRQLFWEKRL QGLSASDVTE QIIKTMELPK GLQGVGPGSN DET LLSAVA SALHTSSAPI TGQVSAAVEK NPAVWLNTSQ PLCKAFIVTD EDIRKQEERV QQVRKKLEEA LMADILSRAA DTEE MDIEM DSGDEA UniProtKB: Methyl-CpG-binding domain protein 2 |
-分子 #2: Metastasis-associated protein MTA1
分子 | 名称: Metastasis-associated protein MTA1 / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 80.904312 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MAANMYRVGD YVYFENSSSN PYLIRRIEEL NKTANGNVEA KVVCFYRRRD ISSTLIALAD KHATLSVCYK AGPGADNGEE GEIEEEMEN PEMVDLPEKL KHQLRHRELF LSRQLESLPA THIRGKCSVT LLNETESLKS YLEREDFFFY SLVYDPQQKT L LADKGEIR ...文字列: MAANMYRVGD YVYFENSSSN PYLIRRIEEL NKTANGNVEA KVVCFYRRRD ISSTLIALAD KHATLSVCYK AGPGADNGEE GEIEEEMEN PEMVDLPEKL KHQLRHRELF LSRQLESLPA THIRGKCSVT LLNETESLKS YLEREDFFFY SLVYDPQQKT L LADKGEIR VGNRYQADIT DLLKEGEEDG RDQSRLETQV WEAHNPLTDK QIDQFLVVAR SVGTFARALD CSSSVRQPSL HM SAAAASR DITLFHAMDT LHKNIYDISK AISALVPQGG PVLCRDEMEE WSASEANLFE EALEKYGKDF TDIQQDFLPW KSL TSIIEY YYMWKTTDRY VQQKRLKAAE AESKLKQVYI PNYNKPNPNQ ISVNNVKAGV VNGTGAPGQS PGAGRACESC YTTQ SYQWY SWGPPNMQCR LCASCWTYWK KYGGLKMPTR LDGERPGPNR SNMSPHGLPA RSSGSPKFAM KTRQAFYLHT TKLTR IARR LCREILRPWH AARHPYLPIN SAAIKAECTA RLPEASQSPL VLKQAVRKPL EAVLRYLETH PRPPKPDPVK SVSSVL SSL TPAKVAPVIN NGSPTILGKR SYEQHNGVDG NMKKRLLMPS RGLANHGQAR HMGPSRNLLL NGKSYPTKVR LIRGGSL PP VKRRRMNWID APDDVFYMAT EETRKIRKLL SSSETKRAAR RPYKPIALRQ SQALPPRPPP PAPVNDEPIV IED UniProtKB: Metastasis-associated protein MTA1 |
-分子 #3: Histone deacetylase 1
分子 | 名称: Histone deacetylase 1 / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO / EC番号: histone deacetylase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 55.178906 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MAQTQGTRRK VCYYYDGDVG NYYYGQGHPM KPHRIRMTHN LLLNYGLYRK MEIYRPHKAN AEEMTKYHSD DYIKFLRSIR PDNMSEYSK QMQRFNVGED CPVFDGLFEF CQLSTGGSVA SAVKLNKQQT DIAVNWAGGL HHAKKSEASG FCYVNDIVLA I LELLKYHQ ...文字列: MAQTQGTRRK VCYYYDGDVG NYYYGQGHPM KPHRIRMTHN LLLNYGLYRK MEIYRPHKAN AEEMTKYHSD DYIKFLRSIR PDNMSEYSK QMQRFNVGED CPVFDGLFEF CQLSTGGSVA SAVKLNKQQT DIAVNWAGGL HHAKKSEASG FCYVNDIVLA I LELLKYHQ RVLYIDIDIH HGDGVEEAFY TTDRVMTVSF HKYGEYFPGT GDLRDIGAGK GKYYAVNYPL RDGIDDESYE AI FKPVMSK VMEMFQPSAV VLQCGSDSLS GDRLGCFNLT IKGHAKCVEF VKSFNLPMLM LGGGGYTIRN VARCWTYETA VAL DTEIPN ELPYNDYFEY FGPDFKLHIS PSNMTNQNTN EYLEKIKQRL FENLRMLPHA PGVQMQAIPE DAIPEESGDE DEDD PDKRI SICSSDKRIA CEEEFSDSEE EGEGGRKNSS NFKKAKRVKT EDEKEKDPEE KKEVTEEEKT KEEKPEAKGV KEEVK LA UniProtKB: Histone deacetylase 1 |
-分子 #4: Histone-binding protein RBBP4
分子 | 名称: Histone-binding protein RBBP4 / タイプ: protein_or_peptide / ID: 4 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 47.709527 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN ...文字列: MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN PDLRLRGHQK EGYGLSWNPN LSGHLLSASD DHTICLWDIS AVPKEGKVVD AKTIFTGHTA VVEDVSWHLL HE SLFGSVA DDQKLMIWDT RSNNTSKPSH SVDAHTAEVN CLSFNPYSEF ILATGSADKT VALWDLRNLK LKLHSFESHK DEI FQVQWS PHNETILASS GTDRRLNVWD LSKIGEEQSP EDAEDGPPEL LFIHGGHTAK ISDFSWNPNE PWVICSVSED NIMQ VWQMA ENIYNDEDPE GSVDPEGQGS UniProtKB: Histone-binding protein RBBP4 |
-分子 #5: INOSITOL HEXAKISPHOSPHATE
分子 | 名称: INOSITOL HEXAKISPHOSPHATE / タイプ: ligand / ID: 5 / コピー数: 2 / 式: IHP |
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分子量 | 理論値: 660.035 Da |
Chemical component information | ChemComp-IHP: |
-分子 #6: ZINC ION
分子 | 名称: ZINC ION / タイプ: ligand / ID: 6 / コピー数: 2 / 式: ZN |
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分子量 | 理論値: 65.409 Da |
-分子 #7: POTASSIUM ION
分子 | 名称: POTASSIUM ION / タイプ: ligand / ID: 7 / コピー数: 4 / 式: K |
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分子量 | 理論値: 39.098 Da |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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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 | 0.1 mg/mL | ||||||||||||
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緩衝液 | pH: 7.5 構成要素:
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 支持フィルム - 材質: GRAPHENE OXIDE / 支持フィルム - トポロジー: HOLEY ARRAY / 前処理 - タイプ: GLOW DISCHARGE / 詳細: 40 mA for 120 sec | ||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV / 詳細: Blot for 3 seconds, blot force 10. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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温度 | 最低: 100.0 K |
特殊光学系 | 位相板: VOLTA PHASE PLATE |
撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 検出モード: COUNTING / デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / 撮影したグリッド数: 1 / 実像数: 1902 / 平均露光時間: 60.0 sec. / 平均電子線量: 34.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 最小 デフォーカス(補正後): 0.5 µm / 倍率(補正後): 129629 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 75000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
初期モデル |
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精密化 | プロトコル: RIGID BODY FIT | ||||||||
得られたモデル | PDB-7aoa: |