+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3114 | |||||||||
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タイトル | Structure of an RNA polymerase II pre-initiation complex | |||||||||
マップデータ | RNA polymerase II pre-initiation complex | |||||||||
試料 |
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キーワード | transcription (転写 (生物学)) / pre-initiation complex / RNA polymerase (RNAポリメラーゼ) / TFIIE / TFIIH (TFIIH) / TFIIB / TBP / TFIIF | |||||||||
機能・相同性 | 機能・相同性情報 regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / regulation of mRNA 3'-end processing / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / positive regulation of mitotic recombination / TFIIH-class transcription factor complex binding ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / regulation of mRNA 3'-end processing / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / positive regulation of mitotic recombination / TFIIH-class transcription factor complex binding / RNA polymerase I general transcription initiation factor binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / transcription open complex formation at RNA polymerase II promoter / regulation of transcription by RNA polymerase III / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 転写開始前複合体 / DNA binding, bending / RNA Polymerase I Transcription Initiation / DNA duplex unwinding / 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 / termination of RNA polymerase II transcription / 3'-5' DNA helicase activity / 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 / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / Estrogen-dependent gene expression / protein phosphatase activator activity / ATPase activator activity / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Dual incision in TC-NER / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / tRNA transcription by RNA polymerase III / RNA polymerase III activity / transcription by RNA polymerase I / transcription by RNA polymerase III / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase I activity / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / DNA修復 / RNA polymerase II activity / RNA polymerase I complex / ATP-dependent activity, acting on DNA / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / positive regulation of RNA polymerase II transcription preinitiation complex assembly / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA helicase activity / transcription antitermination / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / ポリメラーゼ / cytoplasmic stress granule 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (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: 11.0 Å | |||||||||
データ登録者 | Murakami K / Tsai K-L / Kalisman N / Bushnell DA / Asturias FJ / Kornberg RD | |||||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2015 タイトル: Structure of an RNA polymerase II preinitiation complex. 著者: Kenji Murakami / Kuang-Lei Tsai / Nir Kalisman / David A Bushnell / Francisco J Asturias / Roger D Kornberg / 要旨: The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the ...The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription. | |||||||||
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_3114.map.gz | 12.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3114-v30.xml emd-3114.xml | 8.4 KB 8.4 KB | 表示 表示 | EMDBヘッダ |
画像 | image3114.png | 195.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3114 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3114 | 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_3114.map.gz / 形式: CCP4 / 大きさ: 13.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | RNA polymerase II pre-initiation complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.63 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 : yeast RNA polymerase II pre-initiation complex
全体 | 名称: yeast RNA polymerase II pre-initiation complex |
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要素 |
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-超分子 #1000: yeast RNA polymerase II pre-initiation complex
超分子 | 名称: yeast RNA polymerase II pre-initiation complex / タイプ: sample / ID: 1000 / Number unique components: 1 |
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分子量 | 実験値: 1.5 MDa |
-分子 #1: RNA polymerase II pre-initiation complex
分子 | 名称: RNA polymerase II pre-initiation complex / タイプ: protein_or_peptide / ID: 1 / Name.synonym: PIC / 組換発現: No |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) / 別称: yeast |
分子量 | 実験値: 1.5 MDa |
-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 | 0.3 mg/mL |
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緩衝液 | pH: 7.6 詳細: 20 mM HEPES (pH7.6), 5 mM DTT, 2 mM Mg(OAc)2, and 40 mM KOAc |
グリッド | 詳細: 3uL was transferred to Quantifoil and flash frozen in liquid ethane with a Vitrobot. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 120 K / 装置: FEI VITROBOT MARK III |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 22500 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
日付 | 2014年11月14日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 実像数: 2564 / 平均電子線量: 40 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | 詳細: sxcter |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 11.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: sparx / 使用した粒子像数: 7578 |