+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-20281 | |||||||||
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タイトル | The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. | |||||||||
マップデータ | The cryo-EM map of human DNMT3A2/3B3 with NCP. | |||||||||
試料 |
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キーワード | methyltransferase / complex / TRANSFERASE / TRANSFERASE-DNA complex | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programming of gene expression / cellular response to bisphenol A / DNA-methyltransferase activity / protein-cysteine methyltransferase activity / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting ...positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programming of gene expression / cellular response to bisphenol A / DNA-methyltransferase activity / protein-cysteine methyltransferase activity / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / XY body / cellular response to ethanol / response to vitamin A / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / hepatocyte apoptotic process / chromosome, centromeric region / catalytic complex / heterochromatin / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / DNA methylation / response to cocaine / PRC2 methylates histones and DNA / Defective pyroptosis / cellular response to amino acid stimulus / response to lead ion / euchromatin / NoRC negatively regulates rRNA expression / neuron differentiation / response to toxic substance / RMTs methylate histone arginines / nuclear matrix / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / response to estradiol / cellular response to hypoxia / spermatogenesis / methylation / RNA polymerase II-specific DNA-binding transcription factor binding / response to xenobiotic stimulus / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Xenopus laevis (アフリカツメガエル) / synthetic construct (人工物) / 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: 2.94 Å | |||||||||
データ登録者 | Xu TH / Liu M | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nature / 年: 2020 タイトル: Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B. 著者: Ting-Hai Xu / Minmin Liu / X Edward Zhou / Gangning Liang / Gongpu Zhao / H Eric Xu / Karsten Melcher / Peter A Jones / 要旨: CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer. These two DNMTs preferentially ...CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer. These two DNMTs preferentially bind to nucleosomes, yet cannot methylate the DNA wrapped around the nucleosome core, and they favour the methylation of linker DNA at positioned nucleosomes. Here we present the cryo-electron microscopy structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3 and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds to the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur. | |||||||||
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_20281.map.gz | 6.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-20281-v30.xml emd-20281.xml | 22.6 KB 22.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_20281.png | 45.6 KB | ||
Filedesc metadata | emd-20281.cif.gz | 7.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-20281 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20281 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_20281_validation.pdf.gz | 357.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_20281_full_validation.pdf.gz | 356.9 KB | 表示 | |
XML形式データ | emd_20281_validation.xml.gz | 6.9 KB | 表示 | |
CIF形式データ | emd_20281_validation.cif.gz | 7.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20281 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20281 | 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_20281.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | The cryo-EM map of human DNMT3A2/3B3 with NCP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.029 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 : A ternary complex of DNMT3A/B asymmetrically binds to the nucleosomes
+超分子 #1: A ternary complex of DNMT3A/B asymmetrically binds to the nucleosomes
+超分子 #2: Histone
+超分子 #3: DNA (167-MER)
+超分子 #4: DNA (cytosine-5)-methyltransferase
+分子 #1: Histone H3.2
+分子 #2: Histone H4
+分子 #3: Histone H2A type 1
+分子 #4: Histone H2B 1.1
+分子 #7: DNA (cytosine-5)-methyltransferase 3A
+分子 #8: DNA (cytosine-5)-methyltransferase 3B
+分子 #5: DNA (167-MER)
+分子 #6: DNA (167-MER)
+分子 #9: CHLORIDE ION
+分子 #10: S-ADENOSYL-L-HOMOCYSTEINE
-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 | 0.2 mg/mL |
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緩衝液 | pH: 8 |
グリッド | 前処理 - タイプ: GLOW DISCHARGE / 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 65.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm |
試料ステージ | ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |