+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 / pre-initiation complex / RNA polymerase / TFIIE / 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 / RNA polymerase I general transcription initiation factor 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 / 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 / RNA polymerase II core complex assembly / 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 / DNA 3'-5' helicase / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA duplex unwinding / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / DNA binding, bending / 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 / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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 / transcription factor TFIID complex / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / transcription initiation at RNA polymerase III promoter / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / nuclear-transcribed mRNA catabolic process / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / 3'-5' DNA helicase activity / 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 / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / ATPase activator activity / transcription by RNA polymerase III / acetyltransferase activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / positive regulation of RNA polymerase II transcription preinitiation complex assembly / RNA polymerase II activity / positive regulation of transcription initiation by RNA polymerase II / positive regulation of translational initiation / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I complex / RNA polymerase III complex / ATP-dependent activity, acting on DNA / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase II, core complex / translesion synthesis / RNA polymerase II preinitiation complex assembly / DNA helicase activity / translation initiation factor binding / TBP-class protein binding / transcription antitermination / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coregulator activity / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 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 | emd_3114.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 |
-検証レポート
文書・要旨 | emd_3114_validation.pdf.gz | 208.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_3114_full_validation.pdf.gz | 207.9 KB | 表示 | |
XML形式データ | emd_3114_validation.xml.gz | 5.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3114 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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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 |
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 / 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 |
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 |