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基本情報
登録情報 | ![]() | |||||||||
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タイトル | hDEK-nucleosome complex (conformation 1) | |||||||||
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![]() | nucleosome complex / GENE REGULATION | |||||||||
機能・相同性 | ![]() regulation of double-strand break repair via nonhomologous end joining / contractile muscle fiber / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / B-WICH complex / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation ...regulation of double-strand break repair via nonhomologous end joining / contractile muscle fiber / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / B-WICH complex / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / regulation of double-strand break repair / oocyte maturation / positive regulation of transcription by RNA polymerase III / nucleosomal DNA binding / nucleus organization / spermatid development / positive regulation of transcription by RNA polymerase I / single fertilization / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / subtelomeric heterochromatin formation / protein localization to CENP-A containing chromatin / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / viral genome replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / male gonad development / osteoblast differentiation / structural constituent of chromatin / antibacterial humoral response / UCH proteinases / nucleosome / heterochromatin formation / E3 ubiquitin ligases ubiquitinate target proteins / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / defense response to Gram-negative bacterium / Oxidative Stress Induced Senescence / killing of cells of another organism / Estrogen-dependent gene expression / histone binding / transcription by RNA polymerase II / chromosome, telomeric region / cell population proliferation 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.69 Å | |||||||||
![]() | Liu Y / Wang C / Huang H | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: DEK-nucleosome structure shows DEK modulates H3K27me3 and stem cell fate. 著者: Yunfan Shen / Yanhong Liu / Maochao Guo / Song Mao / Rui Chen / Mengran Wang / Zhengbo Li / Yue Li / Wan Chen / Fang Chen / Baixing Wu / Chongyuan Wang / Wei Chen / Huanhuan Cui / Kai Yuan / Hongda Huang / ![]() 要旨: DEK is a highly conserved chromatin-associated oncoprotein that has important roles in regulating chromatin dynamics and stem cell fate. Dysregulation of DEK is associated with stem cell dysfunction ...DEK is a highly conserved chromatin-associated oncoprotein that has important roles in regulating chromatin dynamics and stem cell fate. Dysregulation of DEK is associated with stem cell dysfunction and cancers, including acute myeloid leukemia. Despite its importance in chromatin regulation, the structural mechanisms underlying DEK's interaction with chromatin and its influence on gene regulation remain poorly understood. Here we combined cryogenic electron microscopy (cryo-EM), biochemical and cellular approaches to investigate the molecular mechanisms and functional importance of DEK's interaction with chromatin. Our cryo-EM structures reveal the structural basis of the DEK-nucleosome interaction. Biochemical and cellular results demonstrate that this interaction is crucial for DEK deposition onto chromatin. Furthermore, our results reveal that DEK safeguards mouse embryonic stem cells from acquiring primitive endoderm fates by modulating the repressive histone mark H3K27me3. Together, our study provides crucial molecular insights into the structure and function of DEK, establishing a framework for understanding its roles in chromatin biology and cell fate determination. | |||||||||
履歴 |
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構造の表示
添付画像 |
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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 | ![]() | 91.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 23.7 KB 23.7 KB | 表示 表示 | ![]() |
画像 | ![]() | 113 KB | ||
Filedesc metadata | ![]() | 7 KB | ||
その他 | ![]() ![]() | 165.2 MB 165.2 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 9l1xMC ![]() 9l22C 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 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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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 | ![]() | ||||||||||||||||||||||||||||||||||||
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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: 0.842 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: #1
ファイル | emd_62757_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: #2
ファイル | emd_62757_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 : hDEK-NCP complex conformation 1
全体 | 名称: hDEK-NCP complex conformation 1 |
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要素 |
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-超分子 #1: hDEK-NCP complex conformation 1
超分子 | 名称: hDEK-NCP complex conformation 1 / 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: ![]() |
-分子 #1: Histone H3.3
分子 | 名称: Histone H3.3 / 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: ![]() |
分子量 | 理論値: 15.229787 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: ARTKQTARKS TGGKAPRKQL ATKAARKSAP STGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSAAI GALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA UniProtKB: Histone H3.3 |
-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: ![]() |
分子量 | 理論値: 11.263231 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG 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: ![]() |
分子量 | 理論値: 12.925096 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK 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: ![]() |
分子量 | 理論値: 13.804045 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK UniProtKB: Histone H2B type 1-J |
-分子 #7: Protein DEK
分子 | 名称: Protein DEK / タイプ: protein_or_peptide / ID: 7 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 42.759449 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MSASAPAAEG EGTPTQPASE KEPEMPGPRE ESEEEEDEDD EEEEEEEKEK SLIVEGKREK KKVERLTMQV SSLQREPFTI AQGKGQKLC EIERIHFFLS KKKTDELRNL HKLLYNRPGT VSSLKKNVGQ FSGFPFEKGS VQYKKKEEML KKFRNAMLKS I CEVLDLER ...文字列: MSASAPAAEG EGTPTQPASE KEPEMPGPRE ESEEEEDEDD EEEEEEEKEK SLIVEGKREK KKVERLTMQV SSLQREPFTI AQGKGQKLC EIERIHFFLS KKKTDELRNL HKLLYNRPGT VSSLKKNVGQ FSGFPFEKGS VQYKKKEEML KKFRNAMLKS I CEVLDLER SGVNSELVKR ILNFLMHPKP SGKPLPKSKK TCSKGSKKER NSSGMARKAK RTKCPEILSD ESSSDEDEKK NK EESSDDE DKESEEEPPK KTAKREKPKQ KATSKSKKSV KSANVKKADS STTKKNQNSS KKESESEDSS DDEPLIKKLK KPP TDEELK ETIKKLLASA NLEEVTMKQI CKKVYENYPT YDLTERKDFI KTTVKELIS UniProtKB: Protein DEK |
-分子 #5: 601 DNA_R (189-MER)
分子 | 名称: 601 DNA_R (189-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: ![]() |
分子量 | 理論値: 58.551277 KDa |
配列 | 文字列: (DA)(DT)(DC)(DA)(DG)(DC)(DG)(DA)(DC)(DA) (DC)(DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG) (DA)(DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG) (DA) (DC)(DA)(DC)(DG)(DT) ...文字列: (DA)(DT)(DC)(DA)(DG)(DC)(DG)(DA)(DC)(DA) (DC)(DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG) (DA)(DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG) (DA) (DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC) (DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG) (DG)(DG) (DA)(DG)(DT)(DA)(DA)(DT)(DC) (DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG) (DT)(DT)(DA) (DA)(DA)(DA)(DC)(DG)(DC) (DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC) (DG)(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) (DC)(DT)(DC)(DG)(DA)(DT)(DG)(DG)(DC)(DA) (DT)(DC)(DC)(DG)(DG)(DC)(DA)(DT) (DC) (DA)(DC)(DC)(DC)(DG)(DG)(DA)(DT) |
-分子 #6: 601 DNA (189-MER)
分子 | 名称: 601 DNA (189-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: ![]() |
分子量 | 理論値: 58.154988 KDa |
配列 | 文字列: (DA)(DT)(DC)(DC)(DG)(DG)(DG)(DT)(DG)(DA) (DT)(DG)(DC)(DC)(DG)(DG)(DA)(DT)(DG)(DC) (DC)(DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA) (DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG) (DA)(DG)(DG)(DC)(DC) ...文字列: (DA)(DT)(DC)(DC)(DG)(DG)(DG)(DT)(DG)(DA) (DT)(DG)(DC)(DC)(DG)(DG)(DA)(DT)(DG)(DC) (DC)(DA)(DT)(DC)(DG)(DA)(DG)(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)(DC)(DG)(DC)(DT) (DG)(DT)(DC)(DC) (DC)(DC)(DC)(DG)(DC) (DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG) (DC)(DC)(DA)(DA)(DG) (DG)(DG)(DG)(DA) (DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA) (DG)(DT)(DC)(DT)(DC)(DC) (DA)(DG)(DG) (DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG) (DA)(DT)(DA)(DT)(DA)(DT)(DA) (DC)(DA) (DT)(DC)(DC)(DG)(DA)(DT)(DT)(DC)(DC)(DA) (DG)(DT)(DG)(DC)(DC)(DG)(DG)(DT) (DG) (DT)(DC)(DG)(DC)(DT)(DG)(DA)(DT) |
-分子 #8: UNKNOWN ATOM OR ION
分子 | 名称: UNKNOWN ATOM OR ION / タイプ: ligand / ID: 8 / コピー数: 2 / 式: UNX |
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-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 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 K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: DARK 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): 1.5 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |