登録情報 データベース : EMDB / ID : EMD-40683 ダウンロードとリンクタイトル High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b マップデータ 詳細 試料複合体 : Complex of ESRRB nucleosome bound to OCT4DNA : DNA (168-MER)DNA : DNA (168-MER)タンパク質・ペプチド : Maltodextrin-binding protein,POU domain, class 5, transcription factor 1タンパク質・ペプチド : Histone H3.1タンパク質・ペプチド : Histone H4タンパク質・ペプチド : Histone H2A type 2-Cタンパク質・ペプチド : Histone H2B type 2-Eタンパク質・ペプチド : ScFv 残り4件を表示 表示を減らす 詳細 キーワード nucleosome / transcription factor / transcription / CHROMATIN BINDING PROTEIN-DNA complex / GENE REGULATION / TRANSCRIPTION-DNA complex機能・相同性 機能・相同性情報分子機能 ドメイン・相同性 構成要素
cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / endodermal cell fate specification / Specification of primordial germ cells / heart induction / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation ... cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / endodermal cell fate specification / Specification of primordial germ cells / heart induction / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Specification of the neural plate border / Transcriptional regulation of pluripotent stem cells / Germ layer formation at gastrulation / miRNA binding / somatic stem cell population maintenance / blastocyst development / carbohydrate transmembrane transporter activity / negative regulation of megakaryocyte differentiation / anatomical structure morphogenesis / protein localization to CENP-A containing chromatin / BMP signaling pathway / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / epigenetic regulation of gene expression / 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 / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / negative regulation of miRNA transcription / HCMV Late Events / PRC2 methylates histones and DNA / innate immune response in mucosa / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / nucleosome / sequence-specific double-stranded DNA binding / nucleosome assembly / positive regulation of canonical Wnt signaling pathway / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Processing of DNA double-strand break ends / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / outer membrane-bounded periplasmic space / regulation of gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / defense response to Gram-positive bacterium 類似検索 - 分子機能 POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain ... POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold 類似検索 - ドメイン・相同性 Maltodextrin-binding protein / Histone H4 / Histone H3.1 / POU domain, class 5, transcription factor 1 / Histone H2A type 2-C / Histone H2B type 2-E 類似検索 - 構成要素生物種 Homo sapiens (ヒト) / Escherichia coli (大腸菌)手法 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度 : 3.0 Å 詳細 データ登録者Lian T / Guan R / Bai Y 資金援助 米国, 1件 詳細 詳細を隠すOrganization Grant number 国 National Institutes of Health/National Cancer Institute (NIH/NCI) 米国
引用ジャーナル : Mol Cell / 年 : 2023タイトル : Structural mechanism of LIN28B nucleosome targeting by OCT4.著者 : Ruifang Guan / Tengfei Lian / Bing-Rui Zhou / David Wheeler / Yawen Bai / 要旨 : Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of ... Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing human LIN28B DNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA sequences. Two use their POUS domains while the other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap ∼25 base pair DNA. Our analysis of previous genomic data and determination of the ESRRB-nucleosome-OCT4 structure confirmed the generality of these structural features. Moreover, biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing the LIN28B nucleosome. Thus, our study suggests a mechanism of how OCT4 can target the nucleosome and open closed chromatin. 履歴 登録 2023年5月3日 - ヘッダ(付随情報) 公開 2023年6月28日 - マップ公開 2023年6月28日 - 更新 2023年6月28日 - 現状 2023年6月28日 処理サイト : RCSB / 状態 : 公開
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