+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8ott | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | MYC-MAX bound to a nucleosome at SHL+5.8 | |||||||||
要素 |
| |||||||||
キーワード | TRANSCRIPTION / E-box | |||||||||
機能・相同性 | 機能・相同性情報 Mad-Max complex / SCF ubiquitin ligase complex binding / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / DNA Damage/Telomere Stress Induced Senescence / Regulation of endogenous retroelements by KRAB-ZFP proteins / Recognition and association of DNA glycosylase with site containing an affected purine ...Mad-Max complex / SCF ubiquitin ligase complex binding / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / DNA Damage/Telomere Stress Induced Senescence / Regulation of endogenous retroelements by KRAB-ZFP proteins / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Cleavage of the damaged purine / Metalloprotease DUBs / regulation of cell cycle process / regulation of somatic stem cell population maintenance / HDACs deacetylate histones / PRC2 methylates histones and DNA / UCH proteinases / Binding of TCF/LEF:CTNNB1 to target gene promoters / RNA polymerase II transcription repressor complex / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / negative regulation of cell division / negative regulation of monocyte differentiation / Ub-specific processing proteases / transcription regulator activator activity / response to growth factor / Transcription of E2F targets under negative control by DREAM complex / fibroblast apoptotic process / positive regulation of mesenchymal cell proliferation / negative regulation of stress-activated MAPK cascade / regulation of telomere maintenance / Regulation of NFE2L2 gene expression / protein-DNA complex disassembly / negative regulation of gene expression via chromosomal CpG island methylation / branching involved in ureteric bud morphogenesis / Signaling by ALK / : / E-box binding / : / Transcriptional Regulation by E2F6 / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MLL1 complex / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / chromosome organization / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Cyclin E associated events during G1/S transition / core promoter sequence-specific DNA binding / Packaging Of Telomere Ends / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / 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 / telomere organization / Meiotic synapsis / ERK1 and ERK2 cascade / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / positive regulation of epithelial cell proliferation / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / 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 / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / innate immune response in mucosa / protein-DNA complex / PRC2 methylates histones and DNA / response to gamma radiation / Defective pyroptosis / transcription coregulator binding / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAPK6/MAPK4 signaling / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) 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: 3.3 Å | |||||||||
データ登録者 | Stoos, L. / Michael, A.K. / Kempf, G. / Kater, L. / Cavadini, S. / Thoma, N. | |||||||||
資金援助 | European Union, フランス, 2件
| |||||||||
引用 | ジャーナル: Nature / 年: 2023 タイトル: Cooperation between bHLH transcription factors and histones for DNA access. 著者: Alicia K Michael / Lisa Stoos / Priya Crosby / Nikolas Eggers / Xinyu Y Nie / Kristina Makasheva / Martina Minnich / Kelly L Healy / Joscha Weiss / Georg Kempf / Simone Cavadini / Lukas Kater ...著者: Alicia K Michael / Lisa Stoos / Priya Crosby / Nikolas Eggers / Xinyu Y Nie / Kristina Makasheva / Martina Minnich / Kelly L Healy / Joscha Weiss / Georg Kempf / Simone Cavadini / Lukas Kater / Jan Seebacher / Luca Vecchia / Deyasini Chakraborty / Luke Isbel / Ralph S Grand / Florian Andersch / Jennifer L Fribourgh / Dirk Schübeler / Johannes Zuber / Andrew C Liu / Peter B Becker / Beat Fierz / Carrie L Partch / Jerome S Menet / Nicolas H Thomä / 要旨: The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members. Here we investigate how chromatinized E-boxes are engaged ...The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. ). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry-exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A-H2B acidic patch, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors. | |||||||||
履歴 |
|
-構造の表示
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 | 8ott.cif.gz | 340.7 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb8ott.ent.gz | 257.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8ott.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 | 8ott_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 8ott_full_validation.pdf.gz | 1.3 MB | 表示 | |
XML形式データ | 8ott_validation.xml.gz | 43.2 KB | 表示 | |
CIF形式データ | 8ott_validation.cif.gz | 68.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ot/8ott ftp://data.pdbj.org/pub/pdb/validation_reports/ot/8ott | HTTPS FTP |
-関連構造データ
関連構造データ | 17184MC 8osjC 8oskC 8oslC 8otsC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
---|---|
類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
-タンパク質 , 5種, 8分子 AEBFDHMN
#1: タンパク質 | 分子量: 11179.090 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: 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 (大腸菌) / 参照: UniProt: P68431 #2: タンパク質 | 分子量: 9279.875 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: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...遺伝子: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62805 #4: タンパク質 | 分子量: 10334.827 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: H2BC11, H2BFR, HIST1H2BJ / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P06899 #8: タンパク質 | | 分子量: 6346.392 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: MYC, BHLHE39 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01106 #9: タンパク質 | | 分子量: 6031.737 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: MAX, BHLHD4 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61244 |
---|
-Histone H2A type 1- ... , 2種, 2分子 CG
#3: タンパク質 | 分子量: 11896.886 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: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P04908 |
---|---|
#5: タンパク質 | 分子量: 11807.769 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: H2ac15, Hist1h2ak / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q8CGP7 |
-DNA鎖 , 2種, 2分子 IJ
#6: DNA鎖 | 分子量: 44225.145 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: 44674.430 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, 8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 |
---|
-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 |
| ||||||||||||||||||||||||||||||||||||
由来(天然) |
| ||||||||||||||||||||||||||||||||||||
由来(組換発現) |
| ||||||||||||||||||||||||||||||||||||
緩衝液 | pH: 7.2 | ||||||||||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||||||||
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 / 最大 デフォーカス(公称値): 1800 nm / 最小 デフォーカス(公称値): 800 nm |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) |
-解析
CTF補正 | タイプ: NONE |
---|---|
3次元再構成 | 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 152914 / 対称性のタイプ: POINT |