+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-26258 | |||||||||
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タイトル | structure of LIN28b nucleosome bound 3 OCT4 | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | nucleosome / transcription factor / transcription / CHROMATIN BINDING PROTEIN-DNA complex / TRANSCRIPTION-DNA complex | |||||||||
機能・相同性 | 機能・相同性情報 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 / heterochromatin organization / 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 / 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 / negative regulation of miRNA transcription / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / 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 / gene expression / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response / outer membrane-bounded periplasmic space / Senescence-Associated Secretory Phenotype (SASP) / 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 | |||||||||
生物種 | Homo sapiens (ヒト) / Mus musculus (ハツカネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.6 Å | |||||||||
データ登録者 | Lian T / Guan R / Bai Y | |||||||||
資金援助 | 米国, 1件
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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 |
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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 | emd_26258.map.gz | 6.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-26258-v30.xml emd-26258.xml | 17.5 KB 17.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_26258.png | 55.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-26258 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26258 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_26258_validation.pdf.gz | 386.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_26258_full_validation.pdf.gz | 386.3 KB | 表示 | |
XML形式データ | emd_26258_validation.xml.gz | 6.2 KB | 表示 | |
CIF形式データ | emd_26258_validation.cif.gz | 7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26258 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26258 | 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_26258.map.gz / 形式: CCP4 / 大きさ: 52.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.056 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
-試料の構成要素
-全体 : Complex of nucleosome bound to three OCT-4s
全体 | 名称: Complex of nucleosome bound to three OCT-4s |
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要素 |
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-超分子 #1: Complex of nucleosome bound to three OCT-4s
超分子 | 名称: Complex of nucleosome bound to three OCT-4s / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#8 |
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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: 15.437167 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA |
-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: 11.394426 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG |
-分子 #3: Histone H2A type 2-C
分子 | 名称: Histone H2A type 2-C / 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: 14.017428 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YMAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHKAKSK |
-分子 #4: Histone H2B type 2-E
分子 | 名称: Histone H2B type 2-E / 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: 13.951239 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK |
-分子 #7: Maltodextrin-binding protein,POU domain, class 5, transcription f...
分子 | 名称: Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 タイプ: protein_or_peptide / ID: 7 / コピー数: 3 / 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: 61.269703 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MKEAKIEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKVT VEHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGLL AEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS ALMFNLQEPY F TWPLIAAD ...文字列: MKEAKIEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKVT VEHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGLL AEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS ALMFNLQEPY F TWPLIAAD GGYAFKYENG KYDIKDVGVD NAGAKAGLTF LVDLIKNKHM NADTDYSIAE AAFNKGETAM TINGPWAWSN ID TSKVNYG VTVLP(UNK)FKGQ PSKPFVGVLS AGINAASPNK ELAKEFLENY LLTDEGLEAV NKDKPLGAVA LKSYEEELA KDPRIAATME NAQKGEIMPN IPQMSAFWYA VRTAVINAAS GRQTVDAALA AAQTNAGSEN LYFQGSVDSA AASDIKALQK ELEQFAKLL KQKRITLGYT QADVGLTLGV LFGKVFSQTT ICRFEALQLS FKNMCKLRPL LQKWVEEADN NENLQEICKA E TLVQARKR KRTSIENRVR GNLENLFLQC PKPTLQQISH IAQQLGLEKD VVRVWFCNRR QKGKRSSSEF HHHHHH |
-分子 #8: Single-chain variable fragment
分子 | 名称: Single-chain variable fragment / タイプ: protein_or_peptide / ID: 8 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 29.030146 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ...文字列: MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ASLGERVTIT CKASQDIRSY LSWYQQKPWK SPKTLIYYAT SLADGVPSRF SGSGSGQDFS LTINNLESDD TA TYYCLQH GESPYTFGSG TKLEIKRA |
-分子 #5: DNA (162-MER)
分子 | 名称: DNA (162-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: Homo sapiens (ヒト) |
分子量 | 理論値: 50.398344 KDa |
配列 | 文字列: (DA)(DG)(DT)(DG)(DG)(DT)(DA)(DT)(DT)(DA) (DA)(DC)(DA)(DT)(DA)(DT)(DC)(DC)(DT)(DC) (DA)(DG)(DT)(DG)(DG)(DT)(DG)(DA)(DG) (DT)(DA)(DT)(DT)(DA)(DA)(DC)(DA)(DT)(DG) (DG) (DA)(DA)(DC)(DT)(DT) ...文字列: (DA)(DG)(DT)(DG)(DG)(DT)(DA)(DT)(DT)(DA) (DA)(DC)(DA)(DT)(DA)(DT)(DC)(DC)(DT)(DC) (DA)(DG)(DT)(DG)(DG)(DT)(DG)(DA)(DG) (DT)(DA)(DT)(DT)(DA)(DA)(DC)(DA)(DT)(DG) (DG) (DA)(DA)(DC)(DT)(DT)(DA)(DC)(DT) (DC)(DC)(DA)(DA)(DC)(DA)(DA)(DT)(DA)(DC) (DA)(DG) (DA)(DT)(DG)(DC)(DT)(DG)(DA) (DA)(DT)(DA)(DA)(DA)(DT)(DG)(DT)(DA)(DG) (DT)(DC)(DT) (DA)(DA)(DG)(DT)(DG)(DA) (DA)(DG)(DG)(DA)(DA)(DG)(DA)(DA)(DG)(DG) (DA)(DA)(DA)(DG) (DG)(DT)(DG)(DG)(DG) (DA)(DG)(DC)(DT)(DG)(DC)(DC)(DA)(DT)(DC) (DA)(DC)(DT)(DC)(DA) (DG)(DA)(DA)(DT) (DT)(DG)(DT)(DC)(DC)(DA)(DG)(DC)(DA)(DG) (DG)(DG)(DA)(DT)(DT)(DG) (DT)(DG)(DC) (DA)(DA)(DG)(DC)(DT)(DT)(DG)(DT)(DG)(DA) (DA)(DT)(DA)(DA)(DA)(DG)(DA) (DC)(DA) |
-分子 #6: DNA (162-MER)
分子 | 名称: DNA (162-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: Homo sapiens (ヒト) |
分子量 | 理論値: 49.59568 KDa |
配列 | 文字列: (DT)(DG)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DT) (DC)(DA)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DG) (DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC)(DC) (DT)(DG)(DC)(DT)(DG)(DG)(DA)(DC)(DA)(DA) (DT) (DT)(DC)(DT)(DG)(DA) ...文字列: (DT)(DG)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DT) (DC)(DA)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DG) (DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC)(DC) (DT)(DG)(DC)(DT)(DG)(DG)(DA)(DC)(DA)(DA) (DT) (DT)(DC)(DT)(DG)(DA)(DG)(DT)(DG) (DA)(DT)(DG)(DG)(DC)(DA)(DG)(DC)(DT)(DC) (DC)(DC) (DA)(DC)(DC)(DT)(DT)(DT)(DC) (DC)(DT)(DT)(DC)(DT)(DT)(DC)(DC)(DT)(DT) (DC)(DA)(DC) (DT)(DT)(DA)(DG)(DA)(DC) (DT)(DA)(DC)(DA)(DT)(DT)(DT)(DA)(DT)(DT) (DC)(DA)(DG)(DC) (DA)(DT)(DC)(DT)(DG) (DT)(DA)(DT)(DT)(DG)(DT)(DT)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DG) (DT)(DT)(DC)(DC) (DA)(DT)(DG)(DT)(DT)(DA)(DA)(DT)(DA)(DC) (DT)(DC)(DA)(DC)(DC)(DA) (DC)(DT)(DG) (DA)(DG)(DG)(DA)(DT)(DA)(DT)(DG)(DT)(DT) (DA)(DA)(DT)(DA)(DC)(DC)(DA) (DC)(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 |
-試料調製
緩衝液 | pH: 7.3 |
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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 K3 (6k x 4k) / 平均電子線量: 53.8 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: SPOT SCAN / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.0 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 |
-画像解析
初期モデル | モデルのタイプ: NONE |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 112532 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |