+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3727 | |||||||||
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タイトル | RNA polymerase I pre-initiation complex | |||||||||
マップデータ | ||||||||||
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 core binding / rDNA binding / 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 I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I core binding / rDNA binding / 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 (パン酵母) / synthetic construct (人工物) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.4 Å | |||||||||
データ登録者 | Sadian Y / Tafur L / Kosinski J / Jakobi AJ / Wetzel R / Buczak K / Hagen WJH / Beck M / Sachse C / Muller CW | |||||||||
引用 | ジャーナル: EMBO J / 年: 2017 タイトル: Structural insights into transcription initiation by yeast RNA polymerase I. 著者: Yashar Sadian / Lucas Tafur / Jan Kosinski / Arjen J Jakobi / Rene Wetzel / Katarzyna Buczak / Wim Jh Hagen / Martin Beck / Carsten Sachse / Christoph W Müller / 要旨: In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of ...In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi-subunit pre-initiation complex (PIC) at the ribosomal RNA promoter. In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3, and Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11. Here, we present the cryo-EM structure of the 18-subunit yeast Pol I PIC bound to a transcription scaffold. The cryo-EM map reveals an unexpected arrangement of the DNA and CF subunits relative to Pol I. The upstream DNA is positioned differently than in any previous structures of the Pol II PIC. Furthermore, the TFIIB-related subunit Rrn7 also occupies a different location compared to the Pol II PIC although it uses similar interfaces as TFIIB to contact DNA. Our results show that although general features of eukaryotic transcription initiation are conserved, Pol I and Pol II use them differently in their respective transcription initiation complexes. | |||||||||
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_3727.map.gz | 3.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3727-v30.xml emd-3727.xml | 33.2 KB 33.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_3727.png | 194.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3727 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3727 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_3727_validation.pdf.gz | 213.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_3727_full_validation.pdf.gz | 212.6 KB | 表示 | |
XML形式データ | emd_3727_validation.xml.gz | 6.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3727 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3727 | 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_3727.map.gz / 形式: CCP4 / 大きさ: 91.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.35 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 pre-initiation complex with Core Factor, Rrn3 an...
+超分子 #1: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...
+超分子 #2: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...
+超分子 #3: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...
+分子 #1: RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190
+分子 #2: RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135
+分子 #3: RPA49_YEAST DNA-directed RNA polymerase I subunit
+分子 #4: RPA43_YEAST DNA-directed RNA polymerase I subunit
+分子 #5: RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1
+分子 #6: RPA34_YEAST DNA-directed RNA polymerase I subunit RPA34
+分子 #7: RPAB1_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC1
+分子 #8: RPAB2_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #9: RPAC2_YEAST DNA-directed RNA polymerases I and III subunit RPAC2
+分子 #10: RPAB3_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #11: RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14
+分子 #12: RPA12_YEAST DNA-directed RNA polymerase I subunit RPA12
+分子 #13: RPAB4_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC4
+分子 #14: RPAB5_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #15: RRN3_YEAST RNA polymerase I-specific transcription initiation fac...
+分子 #16: RRN6_YEAST RNA polymerase I-specific transcription initiation fac...
+分子 #17: RRN7_YEAST RNA polymerase I-specific transcription initiation fac...
+分子 #18: RRN11_YEAST RNA polymerase I-specific transcription initiation fa...
+分子 #19: non-template DNA strand
+分子 #20: template DNA strand
-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 | 0.2 mg/mL |
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緩衝液 | pH: 7.5 |
グリッド | 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK II |
-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 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 実像数: 4235 / 平均露光時間: 20.0 sec. / 平均電子線量: 2.0 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): 4.0 µm / 最小 デフォーカス(公称値): 0.75 µm / 倍率(公称値): 105000 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | ソフトウェア - 名称: CTFFIND (ver. 4) |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 1.4) / 使用した粒子像数: 38589 |
初期 角度割当 | タイプ: ANGULAR RECONSTITUTION |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION |