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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: 7wbw | ||||||||||||||||||||||||||||||
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タイトル | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome | ||||||||||||||||||||||||||||||
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![]() | TRANSCRIPTION / RNA / DNA | ||||||||||||||||||||||||||||||
機能・相同性 | ![]() regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / muscle cell differentiation / regulation of transcription elongation by RNA polymerase II / RPB4-RPB7 complex / pericentric heterochromatin formation ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / muscle cell differentiation / regulation of transcription elongation by RNA polymerase II / RPB4-RPB7 complex / pericentric heterochromatin formation / inner kinetochore / transcription elongation factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / oocyte maturation / transcription elongation-coupled chromatin remodeling / 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 / RNA polymerase II complex binding / RNA polymerase III activity / 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 / chromosome, centromeric region / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / single fertilization / transcription elongation by RNA polymerase I / RNA polymerase II activity / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / tRNA transcription by RNA polymerase III / 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 I activity / 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 / transcription elongation factor complex / innate immune response in mucosa / regulation of DNA-templated transcription elongation / PRC2 methylates histones and DNA / Defective pyroptosis / transcription elongation by RNA polymerase II / HDACs deacetylate histones / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / 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 / heterochromatin formation / 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 / 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 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: 7.1 Å | ||||||||||||||||||||||||||||||
![]() | Osumi, K. / Kujirai, T. / Ehara, H. / Sekine, S. / Takizawa, Y. / Kurumizaka, H. | ||||||||||||||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome. 著者: Ken Osumi / Tomoya Kujirai / Haruhiko Ehara / Mitsuo Ogasawara / Chiaki Kinoshita / Mika Saotome / Wataru Kagawa / Shun-Ichi Sekine / Yoshimasa Takizawa / Hitoshi Kurumizaka / ![]() 要旨: In transcription-coupled repair (TCR), transcribing RNA polymerase II (RNAPII) stalls at a DNA lesion and recruits TCR proteins to the damaged site. However, the mechanism by which RNAPII recognizes ...In transcription-coupled repair (TCR), transcribing RNA polymerase II (RNAPII) stalls at a DNA lesion and recruits TCR proteins to the damaged site. However, the mechanism by which RNAPII recognizes a DNA lesion in the nucleosome remains enigmatic. In the present study, we inserted an apurinic/apyrimidinic DNA lesion analogue, tetrahydrofuran (THF), in the nucleosomal DNA, where RNAPII stalls at the SHL(-4), SHL(-3.5), and SHL(-3) positions, and determined the structures of these complexes by cryo-electron microscopy. In the RNAPII-nucleosome complex stalled at SHL(-3.5), the nucleosome orientation relative to RNAPII is quite different from those in the SHL(-4) and SHL(-3) complexes, which have nucleosome orientations similar to naturally paused RNAPII-nucleosome complexes. Furthermore, we found that an essential TCR protein, Rad26 (CSB), enhances the RNAPII processivity, and consequently augments the DNA damage recognition efficiency of RNAPII in the nucleosome. The cryo-EM structure of the Rad26-RNAPII-nucleosome complex revealed that Rad26 binds to the stalled RNAPII through a novel interface, which is completely different from those previously reported. These structures may provide important information to understand the mechanism by which RNAPII recognizes the nucleosomal DNA lesion and recruits TCR proteins to the stalled RNAPII on the nucleosome. | ||||||||||||||||||||||||||||||
履歴 |
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構造の表示
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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ダウンロード
PDBx/mmCIF形式 | ![]() | 1.9 MB | 表示 | ![]() |
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PDB形式 | ![]() | 1.6 MB | 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
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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) ![]() |
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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: 組換発現 / 由来: (組換発現) ![]() ![]() |
#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) ![]() |
-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) ![]() |
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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) ![]() |
#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) ![]() |
#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) ![]() |
-DNA-directed RNA polymerases I, II, and III subunit ... , 2種, 2分子 EH
#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) ![]() |
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#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) ![]() |
-タンパク質 , 5種, 9分子 Faebfcgdh
#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) ![]() | ||||||
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#19: 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) ![]() ![]() ![]() #20: 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: 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, H4-16, HIST4H4 発現宿主: ![]() ![]() #21: 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) ![]() ![]() ![]() #22: 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 polymerase subunit ABC10- ... , 2種, 2分子 JL
#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) ![]() |
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#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) ![]() |
-Transcription elongation factor ... , 3種, 3分子 MVW
#13: タンパク質 | 分子量: 12606.896 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#17: タンパク質 | 分子量: 12039.614 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#18: タンパク質 | 分子量: 101459.422 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
-DNA鎖 , 2種, 2分子 NT
#14: 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) |
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#16: DNA鎖 | 分子量: 60845.949 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
-RNA鎖 , 1種, 1分子 P
#15: RNA鎖 | 分子量: 4969.832 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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-非ポリマー , 2種, 11分子 ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#23: 化合物 | ChemComp-ZN / #24: 化合物 | ChemComp-MG / | |
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-詳細
研究の焦点であるリガンドがあるか | N |
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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 |
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由来(天然) |
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由来(組換発現) | 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 | ||||||||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 56 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.19.2_4158: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 7.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 10400 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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