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データを開く
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基本情報
| 登録情報 | ![]() | |||||||||||||||||||||||||||
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| タイトル | Structure of H1.2 bound to the nucleosome | |||||||||||||||||||||||||||
マップデータ | ||||||||||||||||||||||||||||
試料 |
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キーワード | Nucleosome / Chromatin / DNA / H1.2 / Complex / DNA BINDING PROTEIN | |||||||||||||||||||||||||||
| 機能・相同性 | 機能・相同性情報histone H3K27me3 reader activity / facultative heterochromatin formation / negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / regulation of mRNA splicing, via spliceosome / chromosome condensation / nucleosomal DNA binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation ...histone H3K27me3 reader activity / facultative heterochromatin formation / negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / regulation of mRNA splicing, via spliceosome / chromosome condensation / nucleosomal DNA binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / epigenetic regulation of gene expression / telomere organization / Interleukin-7 signaling / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / innate immune response in mucosa / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / euchromatin / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / chromatin DNA binding / G2/M DNA damage checkpoint / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Metalloprotease DUBs / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / HCMV Early Events / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / double-stranded DNA binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / killing of cells of another organism / defense response to Gram-negative bacterium / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / : / DNA binding / RNA binding / extracellular exosome 類似検索 - 分子機能 | |||||||||||||||||||||||||||
| 生物種 | Homo sapiens (ヒト) / synthetic construct (人工物) | |||||||||||||||||||||||||||
| 手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.0 Å | |||||||||||||||||||||||||||
データ登録者 | Kujirai T / Echigoya K / Takizawa Y / Kurumizaka H | |||||||||||||||||||||||||||
| 資金援助 | 日本, 8件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2025タイトル: Structural insights into how DEK nucleosome binding facilitates H3K27 trimethylation in chromatin. 著者: Tomoya Kujirai / Kenta Echigoya / Yusuke Kishi / Mai Saeki / Tomoko Ito / Junko Kato / Lumi Negishi / Hiroshi Kimura / Hiroshi Masumoto / Yoshimasa Takizawa / Yukiko Gotoh / Hitoshi Kurumizaka / ![]() 要旨: Structural diversity of the nucleosome affects chromatin conformations and regulates eukaryotic genome functions. Here we identify DEK, whose function is unknown, as a nucleosome-binding protein. In ...Structural diversity of the nucleosome affects chromatin conformations and regulates eukaryotic genome functions. Here we identify DEK, whose function is unknown, as a nucleosome-binding protein. In embryonic neural progenitor cells, DEK colocalizes with H3 K27 trimethylation (H3K27me3), the facultative heterochromatin mark. DEK stimulates the methyltransferase activity of Polycomb repressive complex 2 (PRC2), which is responsible for H3K27me3 deposition in vitro. Cryo-electron microscopy structures of the DEK-nucleosome complexes reveal that DEK binds the nucleosome by its tripartite DNA-binding mode on the dyad and linker DNAs and interacts with the nucleosomal acidic patch by its newly identified histone-binding region. The DEK-nucleosome interaction mediates linker DNA reorientation and induces chromatin compaction, which may facilitate PRC2 activation. These findings provide mechanistic insights into chromatin structure-mediated gene regulation by DEK. | |||||||||||||||||||||||||||
| 履歴 |
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構造の表示
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ダウンロードとリンク
-EMDBアーカイブ
| マップデータ | emd_37149.map.gz | 2.8 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-37149-v30.xml emd-37149.xml | 23.8 KB 23.8 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_37149_fsc.xml | 7.2 KB | 表示 | FSCデータファイル |
| 画像 | emd_37149.png | 76.9 KB | ||
| Filedesc metadata | emd-37149.cif.gz | 6.7 KB | ||
| その他 | emd_37149_half_map_1.map.gz emd_37149_half_map_2.map.gz | 23.4 MB 23.4 MB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-37149 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37149 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 8ke0MC ![]() 8kcyC ![]() 8kd1C M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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| 類似構造データ | 類似検索 - 機能・相同性 F&H 検索 |
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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 |
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マップ
| ファイル | ダウンロード / ファイル: emd_37149.map.gz / 形式: CCP4 / 大きさ: 30.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| 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: 1.05 Å | ||||||||||||||||||||||||||||||||||||
| 密度 |
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| 対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
| 詳細 | EMDB XML:
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-添付データ
-ハーフマップ: #2
| ファイル | emd_37149_half_map_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: #1
| ファイル | emd_37149_half_map_2.map | ||||||||||||
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| 投影像・断面図 |
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| 密度ヒストグラム |
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試料の構成要素
-全体 : H1.2 bound to the nucleosome
| 全体 | 名称: H1.2 bound to the nucleosome |
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| 要素 |
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-超分子 #1: H1.2 bound to the nucleosome
| 超分子 | 名称: H1.2 bound to the nucleosome / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#7 |
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| 由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: Histone H3.1
| 分子 | 名称: Histone H3.1 / タイプ: protein_or_peptide / ID: 1 / 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: 15.719445 KDa |
| 組換発現 | 生物種: ![]() |
| 配列 | 文字列: GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA UniProtKB: Histone H3.1 |
-分子 #2: Histone H4
| 分子 | 名称: Histone H4 / 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: 11.676703 KDa |
| 組換発現 | 生物種: ![]() |
| 配列 | 文字列: GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG UniProtKB: Histone H4 |
-分子 #3: Histone H2A type 1-B/E
| 分子 | 名称: Histone H2A type 1-B/E / タイプ: protein_or_peptide / ID: 3 / 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: 14.447825 KDa |
| 組換発現 | 生物種: ![]() |
| 配列 | 文字列: GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK UniProtKB: Histone H2A type 1-B/E |
-分子 #4: Histone H2B type 1-J
| 分子 | 名称: Histone H2B type 1-J / 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: 14.217516 KDa |
| 組換発現 | 生物種: ![]() |
| 配列 | 文字列: GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSAK UniProtKB: Histone H2B type 1-J |
-分子 #7: Histone H1.2
| 分子 | 名称: Histone H1.2 / タイプ: protein_or_peptide / ID: 7 / 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: 22.15684 KDa |
| 組換発現 | 生物種: ![]() |
| 配列 | 文字列: MSETAPAAPA AAPPAEKAPV KKKAAKKAGG TPRKASGPPV SELITKAVAA SKERSGVSLA ALKKALAAAG YDVEKNNSRI KLGLKSLVS KGTLVQTKGT GASGSFKLNK KAASGEAKPK VKKAGGTKPK KPVGAAKKPK KAAGGATPKK SAKKTPKKAK K PAAATVTK ...文字列: MSETAPAAPA AAPPAEKAPV KKKAAKKAGG TPRKASGPPV SELITKAVAA SKERSGVSLA ALKKALAAAG YDVEKNNSRI KLGLKSLVS KGTLVQTKGT GASGSFKLNK KAASGEAKPK VKKAGGTKPK KPVGAAKKPK KAAGGATPKK SAKKTPKKAK K PAAATVTK KVAKSPKKAK VAKPKKAAKS AAKAVKPKAA KPKVVKPKKA APKKKLEVLF Q UniProtKB: Histone H1.2 |
-分子 #5: DNA (193-MER)
| 分子 | 名称: DNA (193-MER) / タイプ: dna / ID: 5 / コピー数: 1 / 分類: DNA |
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| 由来(天然) | 生物種: synthetic construct (人工物) |
| 分子量 | 理論値: 59.589984 KDa |
| 配列 | 文字列: (DA)(DT)(DC)(DA)(DC)(DG)(DT)(DA)(DA)(DT) (DA)(DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DC) (DT)(DA)(DG)(DG)(DA)(DT)(DC)(DA)(DC) (DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG) (DC) (DC)(DG)(DA)(DG)(DG) ...文字列: (DA)(DT)(DC)(DA)(DC)(DG)(DT)(DA)(DA)(DT) (DA)(DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DC) (DT)(DA)(DG)(DG)(DA)(DT)(DC)(DA)(DC) (DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG) (DC) (DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG) (DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT) (DC)(DG) (DT)(DA)(DG)(DA)(DC)(DA)(DG) (DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC) (DG)(DC)(DT) (DT)(DA)(DA)(DA)(DC)(DG) (DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DG)(DA) (DA)(DT)(DC)(DC) (DG)(DT)(DA)(DC)(DG) (DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG) (DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC) (DG)(DA)(DC)(DC)(DA)(DA) (DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG) (DG)(DA) (DT)(DT)(DG)(DT)(DG)(DA)(DT)(DC)(DC)(DT) (DA)(DG)(DC)(DT)(DG)(DG)(DC)(DC) (DA) (DA)(DT)(DA)(DT)(DT)(DA)(DC)(DG)(DT)(DG) (DA)(DT) |
-分子 #6: DNA (193-MER)
| 分子 | 名称: DNA (193-MER) / タイプ: dna / ID: 6 / コピー数: 1 / 分類: DNA |
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| 由来(天然) | 生物種: synthetic construct (人工物) |
| 分子量 | 理論値: 59.580969 KDa |
| 配列 | 文字列: (DA)(DT)(DC)(DA)(DC)(DG)(DT)(DA)(DA)(DT) (DA)(DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DC) (DT)(DA)(DG)(DG)(DA)(DT)(DC)(DA)(DC) (DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG) (DC) (DC)(DG)(DA)(DG)(DG) ...文字列: (DA)(DT)(DC)(DA)(DC)(DG)(DT)(DA)(DA)(DT) (DA)(DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DC) (DT)(DA)(DG)(DG)(DA)(DT)(DC)(DA)(DC) (DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG) (DC) (DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG) (DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT) (DC)(DG) (DT)(DA)(DG)(DA)(DC)(DA)(DG) (DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC) (DG)(DC)(DT) (DT)(DA)(DA)(DA)(DC)(DG) (DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DG)(DA) (DT)(DT)(DC)(DC) (DG)(DT)(DA)(DC)(DG) (DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG) (DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC) (DG)(DA)(DC)(DC)(DA)(DA) (DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG) (DG)(DA) (DT)(DT)(DG)(DT)(DG)(DA)(DT)(DC)(DC)(DT) (DA)(DG)(DC)(DT)(DG)(DG)(DC)(DC) (DA) (DA)(DT)(DA)(DT)(DT)(DA)(DC)(DG)(DT)(DG) (DA)(DT) |
-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 |
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試料調製
| 緩衝液 | pH: 7.5 |
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| 凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
| 顕微鏡 | TFS KRIOS |
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| 撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 56.0 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 / 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 |
| 実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
ムービー
コントローラー
万見について




キーワード
Homo sapiens (ヒト)
データ登録者
日本, 8件
引用






















Z (Sec.)
Y (Row.)
X (Col.)





































解析
FIELD EMISSION GUN

