+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4147 | |||||||||
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タイトル | Yeast RNA polymerase I elongation complex at 3.8A | |||||||||
マップデータ | Sharpened map (B=-149A^2) | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 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 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 / 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 (パン酵母) / Baker's yeast (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: 3.8 Å | |||||||||
データ登録者 | Neyer S / Kunz M / Geiss C / Hantsche M / Hodirnau V-V / Seybert A / Engel C / Scheffer MP / Cramer P / Frangakis AS | |||||||||
引用 | ジャーナル: Nature / 年: 2016 タイトル: Structure of RNA polymerase I transcribing ribosomal DNA genes. 著者: Simon Neyer / Michael Kunz / Christian Geiss / Merle Hantsche / Victor-Valentin Hodirnau / Anja Seybert / Christoph Engel / Margot P Scheffer / Patrick Cramer / Achilleas S Frangakis / 要旨: RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces ...RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme stabilized by a 'connector' element and an expanded cleft containing the active centre in an inactive conformation. The central bridge helix was unfolded and a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The structure of Pol I in its active transcribing conformation has yet to be determined, whereas structures of Pol II and Pol III have been solved with bound DNA template and RNA transcript. Here we report structures of active transcribing Pol I from yeast solved by two different cryo-electron microscopy approaches. A single-particle structure at 3.8 Å resolution reveals a contracted active centre cleft with bound DNA and RNA, and a narrowed pore beneath the active site that no longer holds the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution that was determined from cryo-electron tomograms of Pol I enzymes transcribing cellular rDNA confirms contraction of the cleft and reveals that incoming and exiting rDNA enclose an angle of around 150°. The structures suggest a model for the regulation of transcription elongation in which contracted and expanded polymerase conformations are associated with active and inactive states, respectively. | |||||||||
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_4147.map.gz | 43 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4147-v30.xml emd-4147.xml | 36.7 KB 36.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4147_fsc.xml | 8 KB | 表示 | FSCデータファイル |
画像 | emd_4147.png | 66.1 KB | ||
その他 | emd_4147_additional.map.gz emd_4147_half_map_1.map.gz emd_4147_half_map_2.map.gz | 35.6 MB 35.9 MB 35.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4147 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4147 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4147_validation.pdf.gz | 517.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_4147_full_validation.pdf.gz | 516.9 KB | 表示 | |
XML形式データ | emd_4147_validation.xml.gz | 13.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4147 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4147 | 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_4147.map.gz / 形式: CCP4 / 大きさ: 46.4 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened map (B=-149A^2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-追加マップ: Filtered to 4.2A
ファイル | emd_4147_additional.map | ||||||||||||
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注釈 | Filtered to 4.2A | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Unfiltered half map 1
ファイル | emd_4147_half_map_1.map | ||||||||||||
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注釈 | Unfiltered half map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Unfiltered half map 2
ファイル | emd_4147_half_map_2.map | ||||||||||||
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注釈 | Unfiltered half map 2 | ||||||||||||
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 : Yeast RNA polymerase I elongation complex
+超分子 #1: Yeast RNA polymerase I elongation complex
+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 polymerases I, II, and III subunit RPABC1
+分子 #5: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #6: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #7: DNA-directed RNA polymerase I subunit RPA12
+分子 #8: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #9: DNA-directed RNA polymerases I and III subunit RPAC2
+分子 #10: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+分子 #14: DNA-directed RNA polymerase I subunit RPA49
+分子 #15: DNA-directed RNA polymerase I subunit RPA34
+分子 #16: DNA-directed RNA polymerase I subunit RPA14
+分子 #17: DNA-directed RNA polymerase I subunit RPA43
+分子 #11: template DNA
+分子 #12: non-template DNA
+分子 #13: RNA
+分子 #18: ZINC ION
+分子 #19: MAGNESIUM ION
+分子 #20: SULFATE 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
濃度 | 0.1 mg/mL | ||||||||||||
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緩衝液 | pH: 7.8 構成要素:
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グリッド | モデル: Quantifoil, UltrAuFoil, R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE | ||||||||||||
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 / 詳細: blot force 13, blotting time 8.5s. |
-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 K2 QUANTUM (4k x 4k) 平均電子線量: 56.0 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |