+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6t90 | ||||||
---|---|---|---|---|---|---|---|
タイトル | OCT4-SOX2-bound nucleosome - SHL-6 | ||||||
要素 |
| ||||||
キーワード | TRANSCRIPTION / nucleosome / OCT4 / SOX2 / transcription factor | ||||||
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 / 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 / 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 / endodermal cell fate specification / response to oxygen-glucose deprivation / 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 / Transcriptional Regulation by MECP2 / positive regulation of cell-cell adhesion / 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 / inner ear development / somatic stem cell population maintenance / 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 / Transcriptional and post-translational regulation of MITF-M expression and activity / 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 / 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 / telomere organization / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / bioluminescence / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / negative regulation of miRNA transcription / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / generation of precursor metabolites and energy / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / Deactivation of the beta-catenin transactivating complex / positive regulation of cell differentiation / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / brain development / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / neuron differentiation / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Metalloprotease DUBs / 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 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Aequorea victoria (オワンクラゲ) 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: 3.05 Å | ||||||
データ登録者 | Michael, A.K. / Kempf, G. / Cavadini, S. / Bunker, R.D. / Thoma, N.H. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6t90.cif.gz | 362.4 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb6t90.ent.gz | 264.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6t90.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 6t90_validation.pdf.gz | 908.5 KB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 6t90_full_validation.pdf.gz | 919.6 KB | 表示 | |
XML形式データ | 6t90_validation.xml.gz | 33.4 KB | 表示 | |
CIF形式データ | 6t90_validation.cif.gz | 53.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/t9/6t90 ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t90 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
-タンパク質 , 7種, 10分子 ABFCGDHEKL
#1: タンパク質 | 分子量: 15719.445 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 遺伝子: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: P68431 | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
#2: タンパク質 | 分子量: 11676.703 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 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 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: P62805 #3: タンパク質 | 分子量: 14447.825 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: P04908 #4: タンパク質 | 分子量: 14088.336 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HIST1H2BJ, H2BFR 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: P06899 #5: タンパク質 | | 分子量: 15491.173 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 遺伝子: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...遺伝子: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: P68431 #8: タンパク質 | | 分子量: 70521.289 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Aequorea victoria (オワンクラゲ), (組換発現) Homo sapiens (ヒト) 遺伝子: GFP, POU5F1, OCT3, OCT4, OTF3 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P42212, UniProt: Q01860 #9: タンパク質 | | 分子量: 12718.679 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SOX2 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P48431 |
-DNA鎖 , 2種, 2分子 IJ
#6: DNA鎖 | 分子量: 46961.957 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
---|---|
#7: DNA鎖 | 分子量: 45634.125 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
-非ポリマー , 1種, 9分子
#10: 化合物 | ChemComp-PTD / |
---|
-詳細
研究の焦点であるリガンドがあるか | N |
---|---|
Has protein modification | Y |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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 |
-試料調製
構成要素 |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
分子量 | 実験値: NO | ||||||||||||||||||||||||||||||||||||
由来(天然) |
| ||||||||||||||||||||||||||||||||||||
由来(組換発現) |
| ||||||||||||||||||||||||||||||||||||
緩衝液 | pH: 7.4 | ||||||||||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのタイプ: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 45 e/Å2 フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.17rc2_3619: / 分類: 精密化 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EMソフトウェア | 名称: cryoSPARC / カテゴリ: 3次元再構成 | ||||||||||||||||||||||||
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: 3.05 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 94282 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
|