+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-17184 | |||||||||
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タイトル | MYC-MAX bound to a nucleosome at SHL+5.8 | |||||||||
マップデータ | Map post-processed with LocScale. | |||||||||
試料 |
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キーワード | E-box / TRANSCRIPTION (転写 (生物学)) | |||||||||
機能・相同性 | 機能・相同性情報 Mad-Max complex / SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / Deposition of new CENPA-containing nucleosomes at the centromere / Condensation of Prophase Chromosomes / RNA polymerase II transcription repressor complex / Metalloprotease DUBs / regulation of cell cycle process ...Mad-Max complex / SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / Deposition of new CENPA-containing nucleosomes at the centromere / Condensation of Prophase Chromosomes / RNA polymerase II transcription repressor complex / Metalloprotease DUBs / regulation of cell cycle process / regulation of somatic stem cell population maintenance / UCH proteinases / Binding of TCF/LEF:CTNNB1 to target gene promoters / PRC2 methylates histones and DNA / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / negative regulation of cell division / negative regulation of monocyte differentiation / Ub-specific processing proteases / protein-DNA complex disassembly / transcription regulator activator activity / DNA methylation-dependent heterochromatin formation / Transcription of E2F targets under negative control by DREAM complex / response to growth factor / negative regulation of stress-activated MAPK cascade / regulation of telomere maintenance / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / positive regulation of mesenchymal cell proliferation / branching involved in ureteric bud morphogenesis / Signaling by ALK / E-box binding / Transcriptional Regulation by E2F6 / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / heterochromatin organization / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / MLL1 complex / chromosome organization / nucleosomal DNA binding / 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 / CENP-A containing nucleosome / epigenetic regulation of gene expression / Cyclin E associated events during G1/S transition / Packaging Of Telomere Ends / core promoter sequence-specific DNA binding / negative regulation of fibroblast proliferation / Cyclin A:Cdk2-associated events at S phase entry / 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 / positive regulation of telomerase activity / ERK1 and ERK2 cascade / 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メチル化 / 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) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / positive regulation of epithelial cell proliferation / transcription coregulator binding / HDACs deacetylate histones / デオキシリボ核酸 / response to gamma radiation / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / G1/S transition of mitotic cell cycle / Formation of the beta-catenin:TCF transactivating complex / MAPK6/MAPK4 signaling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / HDMs demethylate histones / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / NOTCH1 Intracellular Domain Regulates Transcription / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines 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 | Stoos L / Michael AK / Kempf G / Kater L / 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_17184.map.gz | 61.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-17184-v30.xml emd-17184.xml | 29.3 KB 29.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_17184_fsc.xml | 10.6 KB | 表示 | FSCデータファイル |
画像 | emd_17184.png | 110.6 KB | ||
その他 | emd_17184_additional_1.map.gz emd_17184_half_map_1.map.gz emd_17184_half_map_2.map.gz | 62.2 MB 115.9 MB 115.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-17184 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17184 | 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_17184.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Map post-processed with LocScale. | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.845 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: Full map.
ファイル | emd_17184_additional_1.map | ||||||||||||
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注釈 | 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_17184_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_17184_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 bound to a nucleosome at SHL+5.8
+超分子 #1: MYC-MAX bound to a nucleosome at SHL+5.8
+超分子 #2: Nucleosomal core particle
+超分子 #3: cMYC/MAX heterodimer
+超分子 #4: Histone octamer
+超分子 #5: Nucleosomal DNA
+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 #5: Histone H2A type 1-K
+分子 #8: Myc proto-oncogene protein
+分子 #9: Protein max
+分子 #6: DNA (144-MER)
+分子 #7: DNA (144-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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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 FIELDBright-field microscopy / 最大 デフォーカス(公称値): 1.8 µm / 最小 デフォーカス(公称値): 0.8 µm |
撮影 | フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 平均電子線量: 50.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |