+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-17183 | |||||||||
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タイトル | OCT4 and MYC-MAX co-bound to a nucleosome | |||||||||
マップデータ | Sharpened map (LocScale) | |||||||||
試料 |
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キーワード | TRANSCRIPTION | |||||||||
機能・相同性 | 機能・相同性情報 Mad-Max complex / SCF ubiquitin ligase complex binding / cell fate commitment involved in formation of primary germ layer / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling ...Mad-Max complex / SCF ubiquitin ligase complex binding / cell fate commitment involved in formation of primary germ layer / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling / endodermal cell fate specification / regulation of asymmetric cell division / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Specification of primordial germ cells / Binding of TCF/LEF:CTNNB1 to target gene promoters / RNA polymerase II transcription repressor complex / heart induction / RUNX3 regulates WNT signaling / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Specification of the neural plate border / TFAP2 (AP-2) family regulates transcription of cell cycle factors / Transcriptional regulation of pluripotent stem cells / negative regulation of cell division / negative regulation of monocyte differentiation / Germ layer formation at gastrulation / transcription regulator activator activity / response to growth factor / Transcription of E2F targets under negative control by DREAM complex / fibroblast apoptotic process / positive regulation of mesenchymal cell proliferation / negative regulation of stress-activated MAPK cascade / miRNA binding / regulation of telomere maintenance / Regulation of NFE2L2 gene expression / protein-DNA complex disassembly / negative regulation of gene expression via chromosomal CpG island methylation / branching involved in ureteric bud morphogenesis / Signaling by ALK / : / E-box binding / : / Transcriptional Regulation by E2F6 / somatic stem cell population maintenance / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / blastocyst development / MLL1 complex / negative regulation of tumor necrosis factor-mediated signaling pathway / anatomical structure morphogenesis / negative regulation of megakaryocyte differentiation / chromosome organization / BMP signaling pathway / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Cyclin E associated events during G1/S transition / core promoter sequence-specific DNA binding / Packaging Of Telomere Ends / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / 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 / telomere organization / Meiotic synapsis / ERK1 and ERK2 cascade / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / bioluminescence / positive regulation of epithelial cell proliferation / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / negative regulation of miRNA transcription / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / innate immune response in mucosa / protein-DNA complex / PRC2 methylates histones and DNA / response to gamma radiation / generation of precursor metabolites and energy / Defective pyroptosis / transcription coregulator binding / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs 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: 3.3 Å | |||||||||
データ登録者 | Michael AK / Stoos L / Kempf G / Cavadini S / Thoma N | |||||||||
資金援助 | European Union, フランス, 2件
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引用 | ジャーナル: Nature / 年: 2023 タイトル: Cooperation between bHLH transcription factors and histones for DNA access. 著者: Alicia K Michael / Lisa Stoos / Priya Crosby / Nikolas Eggers / Xinyu Y Nie / Kristina Makasheva / Martina Minnich / Kelly L Healy / Joscha Weiss / Georg Kempf / Simone Cavadini / Lukas Kater ...著者: Alicia K Michael / Lisa Stoos / Priya Crosby / Nikolas Eggers / Xinyu Y Nie / Kristina Makasheva / Martina Minnich / Kelly L Healy / Joscha Weiss / Georg Kempf / Simone Cavadini / Lukas Kater / Jan Seebacher / Luca Vecchia / Deyasini Chakraborty / Luke Isbel / Ralph S Grand / Florian Andersch / Jennifer L Fribourgh / Dirk Schübeler / Johannes Zuber / Andrew C Liu / Peter B Becker / Beat Fierz / Carrie L Partch / Jerome S Menet / Nicolas H Thomä / 要旨: The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members. Here we investigate how chromatinized E-boxes are engaged ...The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. ). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry-exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A-H2B acidic patch, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors. | |||||||||
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_17183.map.gz | 31.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-17183-v30.xml emd-17183.xml | 31.5 KB 31.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_17183_fsc.xml | 8.9 KB | 表示 | FSCデータファイル |
画像 | emd_17183.png | 83.6 KB | ||
その他 | emd_17183_additional_1.map.gz emd_17183_half_map_1.map.gz emd_17183_half_map_2.map.gz | 32.1 MB 59.4 MB 59.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-17183 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17183 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_17183_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_17183_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_17183_validation.xml.gz | 16.3 KB | 表示 | |
CIF形式データ | emd_17183_validation.cif.gz | 21 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17183 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17183 | 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_17183.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened map (LocScale) | ||||||||||||||||||||||||||||||||||||
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: 0.86 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
-追加マップ: Unsharpened full map
ファイル | emd_17183_additional_1.map | ||||||||||||
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注釈 | Unsharpened full map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map A
ファイル | emd_17183_half_map_1.map | ||||||||||||
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注釈 | Half map A | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map B
ファイル | emd_17183_half_map_2.map | ||||||||||||
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注釈 | Half map B | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : MYC-MAX and OCT4-bound nucleosome
+超分子 #1: MYC-MAX and OCT4-bound nucleosome
+超分子 #2: Nucleosomal core particle
+超分子 #3: Histone octamer
+超分子 #4: Nucleosomal DNA
+超分子 #5: Nucleosome-bound factors
+超分子 #6: OCT4
+超分子 #7: cMYC-MAX heterodimer
+分子 #1: Histone H3.1
+分子 #2: Histone H4
+分子 #3: Histone H2A type 1-B/E
+分子 #4: Histone H2B type 1-J
+分子 #7: Green fluorescent protein,POU domain, class 5, transcription factor 1
+分子 #8: Myc proto-oncogene protein
+分子 #9: Protein max
+分子 #5: DNA (127-MER)
+分子 #6: DNA (127-MER)
+分子 #10: PENTANEDIAL
-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: 7.2 |
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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 K2 SUMMIT (4k x 4k) 平均電子線量: 50.0 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): 0.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |