+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-36251 | |||||||||||||||||||||||||||||||||
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タイトル | RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome | |||||||||||||||||||||||||||||||||
マップデータ | ||||||||||||||||||||||||||||||||||
試料 |
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キーワード | Transcription-DNA-RNA complex / RNAPII / Cryo-EM (低温電子顕微鏡法) | |||||||||||||||||||||||||||||||||
機能・相同性 | 機能・相同性情報 regulation of septum digestion after cytokinesis / regulatory ncRNA-mediated heterochromatin formation / DSIF complex / nuclear DNA-directed RNA polymerase complex / transcription elongation factor activity / RPB4-RPB7 complex / RNA polymerase III activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of DNA-templated transcription, elongation / nucleosomal DNA binding ...regulation of septum digestion after cytokinesis / regulatory ncRNA-mediated heterochromatin formation / DSIF complex / nuclear DNA-directed RNA polymerase complex / transcription elongation factor activity / RPB4-RPB7 complex / RNA polymerase III activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of DNA-templated transcription, elongation / nucleosomal DNA binding / : / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase II activity / chromosome, centromeric region / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / negative regulation of megakaryocyte differentiation / transcription by RNA polymerase III / protein localization to CENP-A containing chromatin / pericentric heterochromatin / RNA polymerase II, core complex / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / translation initiation factor binding / 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 / 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 / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNAメチル化 / DNA-directed RNA polymerase complex / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / regulation of DNA-templated transcription elongation / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / P-body / HDACs deacetylate histones / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / ribonucleoside binding / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / 遺伝的組換え / Pre-NOTCH Transcription and Translation / DNA-directed 5'-3' RNA polymerase activity / ポリメラーゼ / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / ヌクレオソーム / antimicrobial humoral immune response mediated by antimicrobial peptide / single-stranded DNA binding / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) 類似検索 - 分子機能 | |||||||||||||||||||||||||||||||||
生物種 | Komagataella phaffii (菌類) / 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: 5.7 Å | |||||||||||||||||||||||||||||||||
データ登録者 | Akatsu M / Fujita R / Ogasawara M / Ehara H / Kujirai T / Takizawa Y / Sekine S / Kurumizaka H | |||||||||||||||||||||||||||||||||
資金援助 | 日本, 10件
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引用 | ジャーナル: J Biol Chem / 年: 2023 タイトル: Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA. 著者: Munetaka Akatsu / Haruhiko Ehara / Tomoya Kujirai / Risa Fujita / Tomoko Ito / Ken Osumi / Mitsuo Ogasawara / Yoshimasa Takizawa / Shun-Ichi Sekine / Hitoshi Kurumizaka / 要旨: RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the ...RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping. This DNA kink shifts the DNA orientation toward the nucleosome, and the transcribed DNA region interacts with basic amino acid residues of histones H2A, H2B, and H3 exposed by the RNAPII-mediated nucleosomal DNA peeling. The DNA loop structure was not observed in the presence of the transcription elongation factors Spt4/5 and Elf1. These RNAPII-nucleosome structures provide important information for understanding the functional relevance of DNA looping during transcription elongation in the nucleosome. | |||||||||||||||||||||||||||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_36251.map.gz | 13.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-36251-v30.xml emd-36251.xml | 52.9 KB 52.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_36251.png | 91.9 KB | ||
Filedesc metadata | emd-36251.cif.gz | 11.9 KB | ||
その他 | emd_36251_additional_1.map.gz emd_36251_additional_2.map.gz emd_36251_additional_3.map.gz emd_36251_half_map_1.map.gz emd_36251_half_map_2.map.gz | 2 MB 38.2 MB 10.9 MB 140.8 MB 141 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-36251 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36251 | HTTPS FTP |
-関連構造データ
関連構造データ | 8jh2MC 8jh3C 8jh4C M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「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_36251.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: #1
ファイル | emd_36251_additional_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: #2
ファイル | emd_36251_additional_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: #3
ファイル | emd_36251_additional_3.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_36251_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_36251_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : RNA polymerase II - nucleosome complex
+超分子 #1: RNA polymerase II - nucleosome complex
+超分子 #2: RNA polymerase II
+超分子 #3: Histones
+超分子 #4: DNA
+超分子 #5: RNA
+分子 #1: DNA (40-MER)
+分子 #2: DNA (40-MER)
+分子 #16: DNA (218-MER)
+分子 #18: DNA (218-MER)
+分子 #3: DNA-directed RNA polymerase subunit
+分子 #4: DNA-directed RNA polymerase subunit beta
+分子 #5: RNA polymerase II third largest subunit B44, part of central core
+分子 #6: RNA polymerase II subunit B32
+分子 #7: RNA polymerase subunit ABC27
+分子 #8: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
+分子 #9: RNA polymerase II subunit
+分子 #10: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #11: DNA-directed RNA polymerase subunit
+分子 #12: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, I...
+分子 #13: RNA polymerase II subunit B12.5
+分子 #14: RNA polymerase subunit ABC10-alpha
+分子 #15: Transcription elongation factor 1 homolog
+分子 #19: Transcription elongation factor SPT4
+分子 #20: Transcription elongation factor SPT5
+分子 #21: Histone H3.3
+分子 #22: Histone H4
+分子 #23: Histone H2A type 1-B/E
+分子 #24: Histone H2B type 1-J
+分子 #17: RNA (5'-R(P*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')
+分子 #25: ZINC ION
+分子 #26: MAGNESIUM ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.09144 mg/mL | |||||||||||||||
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緩衝液 | pH: 7.5 構成要素:
詳細: 20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl | |||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK III | |||||||||||||||
詳細 | dsDNA concentration is 0.09144 mg/mL. This sample contains 0.005% Tween20. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.0 µm |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 59.84 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: |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 5.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 74079 |