+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10406 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | OCT4-SOX2-bound nucleosome - SHL-6 | |||||||||
マップデータ | ||||||||||
試料 |
| |||||||||
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 / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / adenohypophysis development / regulation of cysteine-type endopeptidase activity involved in apoptotic process / response to oxygen-glucose deprivation ...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 / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / adenohypophysis development / regulation of cysteine-type endopeptidase activity involved in apoptotic process / response to oxygen-glucose deprivation / 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 / negative regulation of cell cycle G1/S phase transition / pituitary gland development / Transcriptional Regulation by MECP2 / positive regulation of cell-cell adhesion / Transcriptional regulation of pluripotent stem cells / regulation of DNA methylation-dependent heterochromatin formation / eye development / 再生 (生物学) / neuronal stem cell population maintenance / 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 / 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 / forebrain development / epigenetic regulation of gene expression / 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 / 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 / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / 生物発光 / DNAメチル化 / Condensation of Prophase Chromosomes / negative regulation of miRNA transcription / 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 / innate immune response in mucosa / generation of precursor metabolites and energy / PRC2 methylates histones and DNA / 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 / negative regulation of canonical Wnt signaling pathway / 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 / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / response to wounding / PKMTs methylate histone lysines / RMTs methylate histone arginines / osteoblast differentiation / 遺伝的組換え / Pre-NOTCH Transcription and Translation / DNA-binding transcription repressor activity, RNA polymerase II-specific / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / structural constituent of chromatin / Transcriptional regulation of granulopoiesis / UCH proteinases / negative regulation of epithelial cell proliferation / ヌクレオソーム / positive regulation of canonical Wnt signaling pathway 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: 3.05 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
| |||||||||
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 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_10406.map.gz | 32.2 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-10406-v30.xml emd-10406.xml | 23.5 KB 23.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_10406.png | 225.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10406 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10406 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_10406.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ボクセルのサイズ | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-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: G protein/GFP fusion protein,POU domain, class 5, transcription f...
+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 #8: Green fluorescent protein,POU domain, class 5, transcription factor 1
+分子 #9: Transcription factor SOX-2
+分子 #6: DNA (146-MER)
+分子 #7: DNA (146-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 |
---|---|
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 |
---|---|
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / 前処理 - タイプ: PLASMA CLEANING |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
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 |
撮影 | フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 平均電子線量: 45.0 e/Å2 |
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: EMDB MAP EMDB ID: |
---|---|
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: RANDOM ASSIGNMENT |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.05 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: cryoSPARC / 使用した粒子像数: 94282 |