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基本情報
登録情報 | データベース: PDB / ID: 6t7b | ||||||||||||
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タイトル | Structure of human Sox2 transcription factor in complex with a nucleosome | ||||||||||||
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![]() | NUCLEAR PROTEIN / Nucleosome / DNA / histones / Sox2 / transcription factor / pioneer factor | ||||||||||||
機能・相同性 | ![]() glial cell fate commitment / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / regulation of cysteine-type endopeptidase activity involved in apoptotic process / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / adenohypophysis development / response to oxygen-glucose deprivation / endodermal cell fate specification / negative regulation of cell cycle G1/S phase transition ...glial cell fate commitment / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / regulation of cysteine-type endopeptidase activity involved in apoptotic process / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / adenohypophysis development / response to oxygen-glucose deprivation / endodermal cell fate specification / 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 / negative regulation of neuron differentiation / 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 / heterochromatin organization / 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 / forebrain development / 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 / 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 / PRC2 methylates histones and DNA / innate immune response in mucosa / Defective pyroptosis / Deactivation of the beta-catenin transactivating complex / HDACs deacetylate histones / positive regulation of cell differentiation / 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 / negative regulation of canonical Wnt signaling pathway / neuron differentiation / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / brain development / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / negative regulation of epithelial cell proliferation / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / 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 / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() synthetic construct (人工物) | ||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 5.1 Å | ||||||||||||
![]() | Dodonova, S.O. / Zhu, F. / Dienemann, C. / Taipale, J. / Cramer, P. | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. 著者: Svetlana O Dodonova / Fangjie Zhu / Christian Dienemann / Jussi Taipale / Patrick Cramer / ![]() ![]() 要旨: 'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions ...'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells. Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription. | ||||||||||||
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 217.8 KB | 表示 | ![]() |
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-検証レポート
文書・要旨 | ![]() | 1.1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.1 MB | 表示 | |
XML形式データ | ![]() | 31.8 KB | 表示 | |
CIF形式データ | ![]() | 51.1 KB | 表示 | |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
-タンパク質 , 5種, 9分子 AEBFCGDHK
#1: タンパク質 | 分子量: 15389.036 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 11394.426 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 遺伝子: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, ...遺伝子: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 プラスミド: pET3a / 発現宿主: ![]() ![]() #3: タンパク質 | 分子量: 16707.277 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #4: タンパク質 | 分子量: 13921.213 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #7: タンパク質 | | 分子量: 10777.620 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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-DNA鎖 , 2種, 2分子 IJ
#5: DNA鎖 | 分子量: 45240.848 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
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#6: DNA鎖 | 分子量: 45484.273 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 |
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分子量 |
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由来(組換発現) |
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ウイルスについての詳細 | 中空か: NO / エンベロープを持つか: NO / 単離: OTHER / タイプ: VIRUS-LIKE PARTICLE | |||||||||||||||||||||||||
天然宿主 | 生物種: Saccharomyces cerevisiae | |||||||||||||||||||||||||
ウイルス殻 | 名称: GAG Capsid / 直径: 480 nm / 三角数 (T数): 9 | |||||||||||||||||||||||||
緩衝液 | pH: 7.5 | |||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.15 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||||||||||||
試料支持 | 詳細: 0.39 mB pressure, 25 mA / グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R2/1 | |||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 289 K 詳細: The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into ...詳細: The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger. |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS 詳細: At least 50% of the data were collected at 25* stage tilt in order to partially compensate for preferred orientation of particles on the grid, and to improve angular distribution. |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 130000 X / 最大 デフォーカス(公称値): 3500 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm / C2レンズ絞り径: 100 µm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 電子線照射量: 1.125 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 撮影したグリッド数: 1 |
電子光学装置 | エネルギーフィルター名称: GIF Bioquantum / エネルギーフィルタースリット幅: 30 eV |
画像スキャン | 動画フレーム数/画像: 40 |
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解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||||||||||||||
3次元再構成 | 解像度: 5.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 32301 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||
EM volume selection | 詳細: 1733 vesicles and near-complete buds were picked from 61 tomograms. Subtomograms were extracted from the surface of the vesicles. Num. of tomograms: 54 / Num. of volumes extracted: 2547 | |||||||||||||||||||||||||||
原子モデル構築 | B value: 100 / プロトコル: OTHER / 空間: REAL | |||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 6FQ5 Accession code: 6FQ5 / Source name: PDB / タイプ: experimental model |