+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10864 | |||||||||
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タイトル | OCT4-SOX2-bound nucleosome - SHL+6 | |||||||||
マップデータ | OCT4-SOX2 bound to SHL 6 | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 glial cell fate commitment / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / cell fate commitment involved in formation of primary germ layer / regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 ...glial cell fate commitment / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / cell fate commitment involved in formation of primary germ layer / regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / response to oxygen-glucose deprivation / endodermal cell fate specification / adenohypophysis development / Specification of primordial germ cells / heart induction / negative regulation of cell cycle G1/S phase transition / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Specification of the neural plate border / pituitary gland development / positive regulation of cell-cell adhesion / Transcriptional Regulation by MECP2 / Transcriptional regulation of pluripotent stem cells / eye development / neuronal stem cell population maintenance / tissue regeneration / Germ layer formation at gastrulation / response to growth factor / miRNA binding / somatic stem cell population maintenance / inner ear development / blastocyst development / negative regulation of neuron differentiation / Transcriptional and post-translational regulation of MITF-M expression and activity / negative regulation of tumor necrosis factor-mediated signaling pathway / anatomical structure morphogenesis / negative regulation of megakaryocyte differentiation / 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 / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / forebrain development / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / 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 / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / bioluminescence / DNA methylation / Condensation of Prophase Chromosomes / negative regulation of miRNA transcription / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / generation of precursor metabolites and energy / Defective pyroptosis / Deactivation of the beta-catenin transactivating complex / HDACs deacetylate histones / positive regulation of cell differentiation / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / 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 / negative regulation of canonical Wnt signaling pathway / brain development / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / heterochromatin formation / neuron differentiation / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / DNA-binding transcription repressor activity, RNA polymerase II-specific / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / response to wounding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin 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: 3.42 Å | |||||||||
データ登録者 | Michael AK / Kempf G / Cavadini S / Bunker RD / Thoma NH | |||||||||
資金援助 | スイス, 1件
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引用 | ジャーナル: Science / 年: 2020 タイトル: Mechanisms of OCT4-SOX2 motif readout on nucleosomes. 著者: Alicia K Michael / Ralph S Grand / Luke Isbel / Simone Cavadini / Zuzanna Kozicka / Georg Kempf / Richard D Bunker / Andreas D Schenk / Alexandra Graff-Meyer / Ganesh R Pathare / Joscha Weiss ...著者: Alicia K Michael / Ralph S Grand / Luke Isbel / Simone Cavadini / Zuzanna Kozicka / Georg Kempf / Richard D Bunker / Andreas D Schenk / Alexandra Graff-Meyer / Ganesh R Pathare / Joscha Weiss / Syota Matsumoto / Lukas Burger / Dirk Schübeler / Nicolas H Thomä / 要旨: Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors ...Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors OCT4 and SOX2 in mouse embryonic stem cells. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling structure determination by cryo-electron microscopy at two preferred positions. Depending on motif location, OCT4 and SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from histone H2A and histone H3; however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA-binding domains to engage DNA in both structures, reading out a partial motif. These findings explain site-specific nucleosome engagement by the pluripotency factors OCT4 and SOX2, and they reveal how TFs distort nucleosomes to access chromatinized motifs. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_10864.map.gz | 32 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10864-v30.xml emd-10864.xml | 24.4 KB 24.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_10864.png | 136.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10864 | 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_10864.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 | OCT4-SOX2 bound to SHL 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : Ternary complex of OCT4-SOX2 and SHL+6 nucleosome
+超分子 #1: Ternary complex of OCT4-SOX2 and SHL+6 nucleosome
+超分子 #2: Histones
+超分子 #3: DNA
+超分子 #4: Green fluorescent protein,POU domain, class 5, transcription factor 1
+超分子 #5: SOX2
+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 H3.1
+分子 #6: Histone H4
+分子 #8: Green fluorescent protein,POU domain, class 5, transcription factor 1
+分子 #9: Transcription factor SOX-2
+分子 #7: DNA (142-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: 7.4 |
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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 QUANTUM (4k x 4k) 検出モード: COUNTING / 平均電子線量: 45.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |