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- EMDB-12721: Yeast TFIIH in the contracted state within the pre-initiation complex -
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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: EMDB / ID: EMD-12721 | ||||||||||||||||||
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タイトル | Yeast TFIIH in the contracted state within the pre-initiation complex | ||||||||||||||||||
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![]() | Pre-initiation complex / TRANSCRIPTION | ||||||||||||||||||
機能・相同性 | ![]() regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter ...regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter / RPB4-RPB7 complex / TFIIH-class transcription factor complex binding / phosphatidylinositol-3-phosphate binding / DNA 3'-5' helicase / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / transcription factor TFIIH holo complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / DNA duplex unwinding / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / nucleolar large rRNA transcription by RNA polymerase I / 3'-5' DNA helicase activity / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / ATPase activator activity / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / ATP-dependent activity, acting on DNA / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / DNA helicase activity / translation initiation factor binding / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / cytoplasmic stress granule / DNA-directed RNA polymerase / ubiquitin protein ligase activity / ribosome biogenesis / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / double-stranded DNA binding / DNA helicase / transcription by RNA polymerase II / damaged DNA binding / single-stranded RNA binding / DNA repair / nucleotide binding / mRNA binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol 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: 3.6 Å | ||||||||||||||||||
![]() | Schilbach S / Aibara S | ||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening. 著者: Sandra Schilbach / Shintaro Aibara / Christian Dienemann / Frauke Grabbe / Patrick Cramer / ![]() 要旨: Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of ...Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of the yeast PIC and define the mechanism of initial DNA opening. We trap the PIC in an intermediate state that contains half a turn of open DNA located 30-35 base pairs downstream of the TATA box. The initially opened DNA region is flanked and stabilized by the polymerase "clamp head loop" and the TFIIF "charged region" that both contribute to promoter-initiated transcription. TFIIE facilitates initiation by buttressing the clamp head loop and by regulating the TFIIH translocase. The initial DNA bubble is then extended in the upstream direction, leading to the open promoter complex and enabling start-site scanning and RNA synthesis. This unique mechanism of DNA opening may permit more intricate regulation than in the Pol I and Pol III systems. | ||||||||||||||||||
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 | EMマップ: ![]() ![]() ![]() |
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 | ![]() | 187.5 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 77 KB 77 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 13.5 KB | 表示 | ![]() |
画像 | ![]() | 83.9 KB | ||
マスクデータ | ![]() | 209.3 MB | ![]() | |
Filedesc metadata | ![]() | 13.8 KB | ||
その他 | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 121.2 MB 95.5 MB 95.8 MB 95.6 MB 95.9 MB 94.3 MB 94.2 MB 96 MB 94.5 MB 94.4 MB 96 MB 95.9 MB 95.9 MB 95.7 MB 95.5 MB 103.1 MB 102.8 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 740.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 740.2 KB | 表示 | |
XML形式データ | ![]() | 20.7 KB | 表示 | |
CIF形式データ | ![]() | 26.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
+マスク #1
+追加マップ: Locally filtered map (non-composite) of a refinement of...
+追加マップ: Half-map 2 of focused refinement encompassing the Tfb2...
+追加マップ: Half-map 2 of focused refinement encompassing the Ssl2/Tfb2/Tfb5...
+追加マップ: Half-map 1 of focused refinement encompassing the Tfb2...
+追加マップ: Half-map 1 of focused refinement encompassing the Ssl2/Tfb2/Tfb5...
+追加マップ: Half-map 1 of focused refinement encompassing the Tfb3-RING-finger/TFIIE/Pol...
+追加マップ: Half-map 2 of focused refinement encompassing the Tfb3-RING-finger/TFIIE/Pol...
+追加マップ: Half-map 1 of focused refinement encompassing the Pol...
+追加マップ: Half-map 1 of focused refinement encompassing the Pol...
+追加マップ: Half-map 2 of focused refinement encompassing the Pol...
+追加マップ: Half-map 2 of focused refinement encompassing the Pol...
+追加マップ: Half-map 1 of focused refinement encompassing the Rad3/Ssl1...
+追加マップ: Half-map 2 of focused refinement encompassing the Rad3/Ssl1...
+追加マップ: Half-map 1 of focused refinement encompassing the Ssl1/Tfb4-eZnF/Tfb1-3-helix-bundle...
+追加マップ: Half-map 2 of focused refinement encompassing the Ssl1/Tfb4-eZnF/Tfb1-3-helix-bundle...
+ハーフマップ: #2
+ハーフマップ: #1
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試料の構成要素
+全体 : Yeast TFIIH in the contracted state within the pre-initiation complex
+超分子 #1: Yeast TFIIH in the contracted state within the pre-initiation complex
+分子 #1: General transcription and DNA repair factor IIH helicase subunit XPD
+分子 #2: General transcription and DNA repair factor IIH subunit TFB1
+分子 #3: General transcription and DNA repair factor IIH subunit TFB2
+分子 #4: RNA polymerase II transcription factor B subunit 3
+分子 #5: General transcription and DNA repair factor IIH subunit TFB4
+分子 #6: General transcription and DNA repair factor IIH subunit TFB5
+分子 #7: General transcription and DNA repair factor IIH subunit SSL1
+分子 #8: General transcription and DNA repair factor IIH helicase subunit XPB
+分子 #9: DNA-directed RNA polymerase II subunit RPB1
+分子 #10: DNA-directed RNA polymerase II subunit RPB2
+分子 #11: DNA-directed RNA polymerase II subunit RPB4
+分子 #12: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #13: DNA-directed RNA polymerase II subunit RPB7
+分子 #16: Transcription initiation factor IIE subunit alpha
+分子 #17: Transcription initiation factor IIE subunit beta
+分子 #14: Non-template DNA
+分子 #15: Template DNA
+分子 #18: IRON/SULFUR CLUSTER
+分子 #19: ZINC ION
+分子 #20: BERYLLIUM TRIFLUORIDE ION
+分子 #21: MAGNESIUM ION
+分子 #22: ADENOSINE-5'-DIPHOSPHATE
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.6 |
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グリッド | モデル: Quantifoil R3.5/1 / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS |
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 IV |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Quantum LS / エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 実像数: 29670 / 平均露光時間: 9.0 sec. / 平均電子線量: 43.6 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 4.0 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 130000 |
試料ステージ | ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |