+
データを開く
-
基本情報
登録情報 | データベース: EMDB / ID: EMD-6980 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA | |||||||||||||||||||||
![]() | whole, postprocessed | |||||||||||||||||||||
![]() |
| |||||||||||||||||||||
![]() | nucleosome / chromatin / RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex | |||||||||||||||||||||
機能・相同性 | ![]() regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / RPB4-RPB7 complex / inner kinetochore / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / RPB4-RPB7 complex / inner kinetochore / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / oocyte maturation / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / nucleus organization / : / : / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase I promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / single fertilization / transcription elongation by RNA polymerase I / negative regulation of megakaryocyte differentiation / positive regulation of translational initiation / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I complex / RNA polymerase III complex / protein localization to CENP-A containing chromatin / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / pericentric heterochromatin / tRNA transcription by RNA polymerase III / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / RNA polymerase I activity / heterochromatin organization / Packaging Of Telomere Ends / RNA polymerase II activity / 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 / translation initiation factor binding / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / 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 / HDACs deacetylate histones / transcription elongation by RNA polymerase II / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / transcription initiation at RNA polymerase II promoter / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / P-body / 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 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / ribonucleoside binding / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / DNA-directed 5'-3' RNA polymerase activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / DNA-directed RNA polymerase / HCMV Early Events / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / male gonad development / nucleosome 類似検索 - 分子機能 | |||||||||||||||||||||
生物種 | ![]() ![]() ![]() | |||||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 5.6 Å | |||||||||||||||||||||
![]() | Kujirai T / Ehara H / Fujino Y / Shirouzu M / Sekine S / Kurumizaka H | |||||||||||||||||||||
資金援助 | ![]()
| |||||||||||||||||||||
![]() | ![]() タイトル: Structural basis of the nucleosome transition during RNA polymerase II passage. 著者: Tomoya Kujirai / Haruhiko Ehara / Yuka Fujino / Mikako Shirouzu / Shun-Ichi Sekine / Hitoshi Kurumizaka / ![]() 要旨: Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo- ...Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation. | |||||||||||||||||||||
履歴 |
|
-
構造の表示
ムービー |
![]() |
---|---|
構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
-
ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 49.1 MB | ![]() | |
---|---|---|---|---|
ヘッダ (付随情報) | ![]() ![]() | 39.9 KB 39.9 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 8.6 KB | 表示 | ![]() |
画像 | ![]() | 88.4 KB | ||
Filedesc metadata | ![]() | 10.6 KB | ||
その他 | ![]() | 49.2 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 566.9 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 566.5 KB | 表示 | |
XML形式データ | ![]() | 10.5 KB | 表示 | |
CIF形式データ | ![]() | 13.7 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 6a5lMC ![]() 6981C ![]() 6982C ![]() 6983C ![]() 6984C ![]() 6985C ![]() 6986C ![]() 6a5oC ![]() 6a5pC ![]() 6a5rC ![]() 6a5tC ![]() 6a5uC ![]() 6inqC 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 ( |
---|---|
類似構造データ |
-
リンク
EMDBのページ | ![]() ![]() |
---|---|
「今月の分子」の関連する項目 |
-
マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | whole, postprocessed | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.49 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-追加マップ: nucleosome, postprocessed
ファイル | emd_6980_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | nucleosome, postprocessed | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-
試料の構成要素
+全体 : RNA polymerase II elongation complex stalled at SHL(-1) of the nu...
+超分子 #1: RNA polymerase II elongation complex stalled at SHL(-1) of the nu...
+分子 #1: DNA-directed RNA polymerase subunit
+分子 #2: DNA-directed RNA polymerase subunit beta
+分子 #3: RNA polymerase II third largest subunit B44, part of central core
+分子 #4: RNA polymerase II subunit B32
+分子 #5: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
+分子 #6: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
+分子 #7: RNA polymerase II subunit
+分子 #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #9: DNA-directed RNA polymerase subunit
+分子 #10: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, I...
+分子 #11: RNA polymerase II subunit B12.5
+分子 #12: RNA polymerase subunit ABC10-alpha
+分子 #16: Histone H3.3
+分子 #17: Histone H4
+分子 #18: Histone H2A type 1-B/E
+分子 #19: Histone H2B type 1-J
+分子 #13: RNA (5'-R(P*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*G)-3')
+分子 #14: DNA (198-MER)
+分子 #15: DNA (198-MER)
+分子 #20: DNA (42-MER)
+分子 #21: DNA (42-MER)
+分子 #22: ZINC ION
+分子 #23: MAGNESIUM ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
![]() | 単粒子再構成法 |
試料の集合状態 | particle |
-
試料調製
緩衝液 | pH: 7.5 |
---|---|
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 298 K / 装置: FEI VITROBOT MARK IV |
-
電子顕微鏡法
顕微鏡 | FEI TECNAI ARCTICA |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Talos Arctica / 画像提供: FEI Company |
+
画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
---|---|
得られたモデル | ![]() PDB-6a5l: |