+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-19726 | |||||||||
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タイトル | RNA polymerase II early elongation complex bound to TFIIE and TFIIF - state a (composite structure) | |||||||||
マップデータ | Composite map for model building of EC14a (sharpened) | |||||||||
試料 |
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キーワード | RNA polymerase II / promoter escape / de novo transcription / TRANSCRIPTION | |||||||||
機能・相同性 | 機能・相同性情報 transcription factor TFIIE complex / phosphatase activator activity / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing ...transcription factor TFIIE complex / phosphatase activator activity / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription factor TFIIF complex / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase III activity / mRNA Splicing - Minor Pathway / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / translation initiation factor binding / mRNA Splicing - Major Pathway / negative regulation of protein binding / TP53 Regulates Transcription of DNA Repair Genes / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / P-body / response to virus / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / microtubule cytoskeleton / cell junction / single-stranded DNA binding / protein phosphatase binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / nucleic acid binding / chromosome, telomeric region / single-stranded RNA binding / protein dimerization activity / nuclear speck / protein domain specific binding / intracellular membrane-bounded organelle / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / chromatin binding 類似検索 - 分子機能 | |||||||||
生物種 | Sus scrofa (ブタ) / unidentified adenovirus (ウイルス) / Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | |||||||||
データ登録者 | Zhan Y / Grabbe F / Oberbeckmann E / Dienemann C / Cramer P | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Mol Cell / 年: 2024 タイトル: Three-step mechanism of promoter escape by RNA polymerase II. 著者: Yumeng Zhan / Frauke Grabbe / Elisa Oberbeckmann / Christian Dienemann / Patrick Cramer / 要旨: The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how ...The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase II (RNA Pol II) and initiation factors are broken to enable promoter escape. Here, we reconstitute RNA Pol II promoter escape in vitro and determine high-resolution structures of initially transcribing complexes containing 8-, 10-, and 12-nt ordered RNAs and two elongation complexes containing 14-nt RNAs. We suggest that promoter escape occurs in three major steps. First, the growing RNA displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, the rewinding of the transcription bubble coincides with the eviction of TFIIA, TFIIB, and TBP. Third, the binding of DSIF and NELF facilitates TFIIE and TFIIH dissociation, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of RNA Pol II transcription. | |||||||||
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_19726.map.gz | 213.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-19726-v30.xml emd-19726.xml | 51.7 KB 51.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_19726.png | 128.2 KB | ||
マスクデータ | emd_19726_msk_1.map | 244.1 MB | マスクマップ | |
Filedesc metadata | emd-19726.cif.gz | 11.4 KB | ||
その他 | emd_19726_additional_1.map.gz emd_19726_additional_2.map.gz emd_19726_additional_3.map.gz emd_19726_additional_4.map.gz emd_19726_additional_5.map.gz emd_19726_additional_6.map.gz emd_19726_additional_7.map.gz | 194.3 MB 193.8 MB 140.7 MB 619.2 KB 193.6 MB 194.2 MB 140.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-19726 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19726 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_19726_validation.pdf.gz | 428.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_19726_full_validation.pdf.gz | 428.1 KB | 表示 | |
XML形式データ | emd_19726_validation.xml.gz | 7.2 KB | 表示 | |
CIF形式データ | emd_19726_validation.cif.gz | 8.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19726 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19726 | HTTPS FTP |
-関連構造データ
-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_19726.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Composite map for model building of EC14a (sharpened) | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
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:
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-添付データ
-マスク #1
ファイル | emd_19726_msk_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: Half map corresponding to the map focused refined on EC14a.
ファイル | emd_19726_additional_1.map | ||||||||||||
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注釈 | Half map corresponding to the map focused refined on EC14a. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Half map corresponding to the map focused refined on EC14a.
ファイル | emd_19726_additional_2.map | ||||||||||||
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注釈 | Half map corresponding to the map focused refined on EC14a. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Focused refined map of EC14a (locally filtered).
ファイル | emd_19726_additional_3.map | ||||||||||||
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注釈 | Focused refined map of EC14a (locally filtered). | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Mask for focused refinement on Pol II
ファイル | emd_19726_additional_4.map | ||||||||||||
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注釈 | Mask for focused refinement on Pol II | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Half map corresponding to the map focused refined on Pol II
ファイル | emd_19726_additional_5.map | ||||||||||||
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注釈 | Half map corresponding to the map focused refined on Pol II | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Half map corresponding to the map focused refined on Pol II.
ファイル | emd_19726_additional_6.map | ||||||||||||
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注釈 | Half map corresponding to the map focused refined on Pol II. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Focused refined map of Pol II (locally filtered).
ファイル | emd_19726_additional_7.map | ||||||||||||
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注釈 | Focused refined map of Pol II (locally filtered). | ||||||||||||
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 early elongation complex bound to TFIIE and TFI...
+超分子 #1: RNA polymerase II early elongation complex bound to TFIIE and TFI...
+超分子 #2: RNA polymerase II
+超分子 #3: DNA and RNA
+超分子 #4: Transcription factor IIE and IIF
+分子 #1: DNA-directed RNA polymerase subunit
+分子 #2: DNA-directed RNA polymerase subunit beta
+分子 #3: DNA-directed RNA polymerase II subunit RPB3
+分子 #4: RNA polymerase II subunit D
+分子 #5: DNA-directed RNA polymerase II subunit E
+分子 #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #7: DNA-directed RNA polymerase II subunit RPB7
+分子 #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #9: DNA-directed RNA polymerase II subunit RPB9
+分子 #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #11: DNA-directed RNA polymerase II subunit RPB11-a
+分子 #12: RNA polymerase II subunit K
+分子 #15: General transcription factor IIF subunit 1
+分子 #16: General transcription factor IIF subunit 2
+分子 #18: General transcription factor IIE subunit 1
+分子 #19: Transcription initiation factor IIE subunit beta
+分子 #13: Non-template DNA
+分子 #17: Template DNA
+分子 #14: RNA
+分子 #20: ZINC ION
+分子 #21: 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
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 40.0 e/Å2 |
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 FIELD / 最大 デフォーカス(公称値): 1.7 µm 最小 デフォーカス(公称値): 0.7000000000000001 µm |
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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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF 詳細: Number of particles is different for every focused refined map, as detailed in the manuscript. 使用した粒子像数: 50000 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |