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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 6a5p | |||||||||||||||||||||
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タイトル | RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome | |||||||||||||||||||||
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![]() | TRANSCRIPTION/RNA/DNA / 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 / RPB4-RPB7 complex / pericentric heterochromatin formation / inner kinetochore / oocyte maturation ...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 / RPB4-RPB7 complex / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / nucleus organization / termination of RNA polymerase I transcription / RNA polymerase III activity / 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 / RNA polymerase II activity / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / transcription elongation by RNA polymerase I / single fertilization / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / negative regulation of megakaryocyte differentiation / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / protein localization to CENP-A containing chromatin / RNA polymerase II, core complex / pericentric heterochromatin / 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 / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / translation initiation factor 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 / 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 / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / transcription elongation by RNA polymerase II / Transcriptional regulation by small RNAs / P-body / 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 / multicellular organism growth / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / heterochromatin formation / DNA Damage/Telomere Stress Induced Senescence / ribonucleoside binding / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / male gonad development / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins 類似検索 - 分子機能 | |||||||||||||||||||||
生物種 | ![]() ![]() 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: 7 Å | |||||||||||||||||||||
![]() | Kujirai, T. / Ehara, H. / Fujino, Y. / Shirouzu, M. / Sekine, S. / Kurumizaka, H. | |||||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() 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 |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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PDBx/mmCIF形式 | ![]() | 1018.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 800.5 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 6982MC ![]() 6980C ![]() 6981C ![]() 6983C ![]() 6984C ![]() 6985C ![]() 6986C ![]() 6a5lC ![]() 6a5oC ![]() 6a5rC ![]() 6a5tC ![]() 6a5uC ![]() 6inqC 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 ( |
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類似構造データ | |
電子顕微鏡画像生データ | ![]() Data size: 1.4 TB Data #1: Unaligned movies of RNA polymerase II transcribing a nucleosome [micrographs - multiframe]) |
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リンク
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集合体
登録構造単位 | ![]()
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要素
-DNA-directed RNA polymerase ... , 3種, 3分子 ABI
#1: タンパク質 | 分子量: 194107.422 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: GS115 / ATCC 20864 / 参照: UniProt: C4R4Y0, DNA-directed RNA polymerase |
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#2: タンパク質 | 分子量: 139746.094 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: GS115 / ATCC 20864 / 参照: UniProt: C4QZQ7, DNA-directed RNA polymerase |
#9: タンパク質 | 分子量: 13612.320 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: GS115 / ATCC 20864 / 参照: UniProt: F2QPE6 |
-RNA polymerase II ... , 4種, 4分子 CDGK
#3: タンパク質 | 分子量: 34216.293 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: GS115 / ATCC 20864 / 参照: UniProt: C4R7L2 |
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#4: タンパク質 | 分子量: 20622.980 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: GS115 / ATCC 20864 / 参照: UniProt: C4R2U9 |
#7: タンパク質 | 分子量: 18802.625 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: GS115 / ATCC 20864 / 参照: UniProt: C4R9A1 |
#11: タンパク質 | 分子量: 13832.896 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: GS115 / ATCC 20864 / 参照: UniProt: C4R3Z5 |
-RNA polymerase subunit ... , 4種, 4分子 EFJL
#5: タンパク質 | 分子量: 24962.680 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: GS115 / ATCC 20864 / 参照: UniProt: C4R3P8 |
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#6: タンパク質 | 分子量: 17803.588 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: GS115 / ATCC 20864 / 参照: UniProt: C4R1V1 |
#10: タンパク質 | 分子量: 8554.064 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: GS115 / ATCC 20864 / 参照: UniProt: C4R009 |
#12: タンパク質 | 分子量: 7862.048 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: GS115 / ATCC 20864 / 参照: UniProt: F2QMI1 |
-タンパク質 , 5種, 9分子 Haebfcgdh
#8: タンパク質 | 分子量: 16249.220 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: GS115 / ATCC 20864 / 参照: UniProt: C4R273 | ||||||
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#16: タンパク質 | 分子量: 15643.262 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #17: 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) ![]() 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: ![]() ![]() #18: 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) ![]() ![]() ![]() #19: タンパク質 | 分子量: 14217.516 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
-RNA鎖 , 1種, 1分子 P
#13: RNA鎖 | 分子量: 3595.162 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: produced by in vitro transcription / 由来: (合成) synthetic construct (人工物) |
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-DNA鎖 , 2種, 2分子 TN
#14: DNA鎖 | 分子量: 60869.977 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
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#15: DNA鎖 | 分子量: 61381.906 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 , 2種, 9分子 ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#20: 化合物 | ChemComp-ZN / #21: 化合物 | ChemComp-MG / | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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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 |
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試料調製
構成要素 | 名称: RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome タイプ: COMPLEX / Entity ID: #1-#19 / 由来: MULTIPLE SOURCES |
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分子量 | 実験値: NO |
由来(天然) | 生物種: ![]() |
緩衝液 | pH: 7.5 |
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 / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 298 K |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Talos Arctica / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI ARCTICA |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 50 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
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解析
EMソフトウェア |
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CTF補正 | タイプ: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 91888 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL |