- EMDB-10393: Structure of two copies of human Sox11 transcription factor in co... -
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基本情報
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データベース: EMDB / ID: EMD-10393
タイトル
Structure of two copies of human Sox11 transcription factor in complex with a nucleosome
マップデータ
Structure of two copies of human Sox11 transcription factor in complex with a nucleosome
試料
複合体: Structure of two copies of human Sox11 transcription factor in complex with a nucleosome
複合体: Histones and Sox11
タンパク質・ペプチド: Histone H3.2
タンパク質・ペプチド: Histone H4
タンパク質・ペプチド: Histone H2A type 1-B/E
タンパク質・ペプチド: Histone H2B type 1-K
タンパク質・ペプチド: Transcription factor SOX-11
複合体: DNA
DNA: DNA (147-MER)
DNA: DNA (147-MER)
キーワード
Nucleosome / DNA / histones / Sox11 / transcription factor / pioneer factor / NUCLEAR PROTEIN
機能・相同性
機能・相同性情報
closure of optic fissure / positive regulation of lens epithelial cell proliferation / soft palate development / cornea development in camera-type eye / positive regulation of hippo signaling / noradrenergic neuron differentiation / negative regulation of transcription regulatory region DNA binding / negative regulation of lymphocyte proliferation / hard palate development / lens morphogenesis in camera-type eye ...closure of optic fissure / positive regulation of lens epithelial cell proliferation / soft palate development / cornea development in camera-type eye / positive regulation of hippo signaling / noradrenergic neuron differentiation / negative regulation of transcription regulatory region DNA binding / negative regulation of lymphocyte proliferation / hard palate development / lens morphogenesis in camera-type eye / embryonic skeletal system morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / embryonic digestive tract morphogenesis / neuroepithelial cell differentiation / camera-type eye morphogenesis / oligodendrocyte development / sympathetic nervous system development / positive regulation of hormone secretion / positive regulation of BMP signaling pathway / positive regulation of ossification / positive regulation of neurogenesis / negative regulation of glial cell proliferation / ventricular septum morphogenesis / spinal cord development / lung morphogenesis / positive regulation of stem cell proliferation / eyelid development in camera-type eye / outflow tract morphogenesis / skeletal muscle cell differentiation / negative regulation of megakaryocyte differentiation / heterochromatin organization / glial cell proliferation / protein localization to CENP-A containing chromatin / positive regulation of osteoblast differentiation / 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 / 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 / Meiotic synapsis / telomere organization / positive regulation of neuron differentiation / 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 / innate immune response in mucosa / PRC2 methylates histones and DNA / kidney development / Defective pyroptosis / HDACs deacetylate histones / 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 / 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 / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / 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 / nervous system development / 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) / DNA-binding transcription activator activity, RNA polymerase II-specific 類似検索 - 分子機能
Transcription factor SOX-12/11/4 / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site ...Transcription factor SOX-12/11/4 / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold 類似検索 - ドメイン・相同性
ジャーナル: Nature / 年: 2020 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.
凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 289 K / 装置: FEI VITROBOT MARK IV 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..
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.