+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8777 | ||||||||||||||||||
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タイトル | Pol I Initial Transcribing Complex with a truncated scaffold at 6.9 angstrom | ||||||||||||||||||
マップデータ | RNA polymerase I Initial Transcribing Complex with a truncated scaffold | ||||||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE ...RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / regulation of cell size / 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 / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / TBP-class protein binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / ribosome biogenesis / peroxisome / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Saccharomyces cerevisiae S288c (パン酵母) | ||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.9 Å | ||||||||||||||||||
データ登録者 | Han Y / He Y | ||||||||||||||||||
資金援助 | 米国, 5件
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引用 | ジャーナル: Elife / 年: 2017 タイトル: Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. 著者: Yan Han / Chunli Yan / Thi Hoang Duong Nguyen / Ashleigh J Jackobel / Ivaylo Ivanov / Bruce A Knutson / Yuan He / 要旨: Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a ...Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC. | ||||||||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
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 | emd_8777.map.gz | 1.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-8777-v30.xml emd-8777.xml | 33.7 KB 33.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_8777_fsc.xml | 4.7 KB | 表示 | FSCデータファイル |
画像 | emd_8777.png | 135.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8777 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8777 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_8777_validation.pdf.gz | 79.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_8777_full_validation.pdf.gz | 78.3 KB | 表示 | |
XML形式データ | emd_8777_validation.xml.gz | 495 B | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8777 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8777 | 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_8777.map.gz / 形式: CCP4 / 大きさ: 8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | RNA polymerase I Initial Transcribing Complex with a truncated scaffold | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.36 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
-試料の構成要素
+全体 : RNA Polymerase I Initial Transcribing Complex with a truncated sc...
+超分子 #1: RNA Polymerase I Initial Transcribing Complex with a truncated sc...
+分子 #1: DNA-directed RNA polymerase I subunit RPA190
+分子 #2: DNA-directed RNA polymerase I subunit RPA135
+分子 #3: DNA-directed RNA polymerases I and III subunit RPAC1
+分子 #4: DNA-directed RNA polymerase I subunit RPA14
+分子 #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+分子 #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #7: DNA-directed RNA polymerase I subunit RPA43
+分子 #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #9: DNA-directed RNA polymerase I subunit RPA12
+分子 #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #11: DNA-directed RNA polymerases I and III subunit RPAC2
+分子 #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+分子 #13: DNA-directed RNA polymerase I subunit RPA49
+分子 #14: DNA-directed RNA polymerase I subunit RPA34
+分子 #15: RNA polymerase I-specific transcription initiation factor RRN6
+分子 #16: RNA polymerase I-specific transcription initiation factor RRN7
+分子 #17: RNA polymerase I-specific transcription initiation factor RRN11
+分子 #18: RNA
+分子 #19: template strand DNA
+分子 #20: upstream non-template strand DNA
+分子 #21: downstream non-template strand DNA
-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: 7.6 |
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グリッド | モデル: Quantifoil S7/2 / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 雰囲気: AIR |
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 |
-電子顕微鏡法
顕微鏡 | JEOL 3200FS |
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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 / 平均露光時間: 12.0 sec. / 平均電子線量: 17.2 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 最大 デフォーカス(補正後): 5.0 µm / 最小 デフォーカス(補正後): 2.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.0 mm / 倍率(公称値): 15000 |
試料ステージ | 試料ホルダーモデル: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER ホルダー冷却材: NITROGEN |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
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