+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7o75 | ||||||||||||||||||
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タイトル | Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA | ||||||||||||||||||
要素 |
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キーワード | TRANSCRIPTION / Pre-initiation complex | ||||||||||||||||||
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 / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / regulation of transcription by RNA polymerase III ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / DNA 5'-3' helicase / transcription factor TFIIF complex / transcription factor TFIIA complex / phosphatidylinositol-3-phosphate binding / RNA polymerase I preinitiation complex assembly / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 3'-5' helicase / transcription preinitiation complex / DNA binding, bending / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / DNA duplex unwinding / poly(A)+ mRNA export from nucleus / 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 / 3'-5' DNA helicase activity / TP53 Regulates Transcription of DNA Repair Genes / transcription factor TFIID complex / 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 / RNA polymerase II general transcription initiation factor activity / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / RNA Polymerase I Promoter Escape / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / ATPase activator activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Estrogen-dependent gene expression / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription-coupled nucleotide-excision repair / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / ATP-dependent activity, acting on DNA / positive regulation of translational initiation / translesion synthesis / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA helicase activity / isomerase activity / DNA-templated transcription initiation / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / transcription coregulator activity / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Saccharomyces cerevisiae S288C (パン酵母) Saccharomyces cerevisiae (パン酵母) Saccharomyces cerevisiae YJM984 (パン酵母) | ||||||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.2 Å | ||||||||||||||||||
データ登録者 | Schilbach, S. / Aibara, S. / Dienemann, C. / Grabbe, F. / Cramer, P. | ||||||||||||||||||
資金援助 | ドイツ, 5件
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引用 | ジャーナル: Cell / 年: 2021 タイトル: Structure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening. 著者: Sandra Schilbach / Shintaro Aibara / Christian Dienemann / Frauke Grabbe / Patrick Cramer / 要旨: Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of ...Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of the yeast PIC and define the mechanism of initial DNA opening. We trap the PIC in an intermediate state that contains half a turn of open DNA located 30-35 base pairs downstream of the TATA box. The initially opened DNA region is flanked and stabilized by the polymerase "clamp head loop" and the TFIIF "charged region" that both contribute to promoter-initiated transcription. TFIIE facilitates initiation by buttressing the clamp head loop and by regulating the TFIIH translocase. The initial DNA bubble is then extended in the upstream direction, leading to the open promoter complex and enabling start-site scanning and RNA synthesis. This unique mechanism of DNA opening may permit more intricate regulation than in the Pol I and Pol III systems. | ||||||||||||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7o75.cif.gz | 1.7 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7o75.ent.gz | 1.3 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7o75.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 7o75_validation.pdf.gz | 1.4 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7o75_full_validation.pdf.gz | 1.5 MB | 表示 | |
XML形式データ | 7o75_validation.xml.gz | 217.7 KB | 表示 | |
CIF形式データ | 7o75_validation.cif.gz | 338.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/o7/7o75 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/7o75 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
+General transcription and DNA repair factor IIH helicase subunit ... , 2種, 2分子 07
+General transcription and DNA repair factor IIH subunit ... , 5種, 5分子 12456
+タンパク質 , 3種, 3分子 3MO
+DNA-directed RNA polymerase II subunit ... , 7種, 7分子 ABCDGIK
+DNA-directed RNA polymerases I, II, and III subunit ... , 5種, 5分子 EFHJL
+DNA鎖 , 2種, 2分子 NT
+Transcription initiation factor IIF subunit ... , 2種, 2分子 QR
+Transcription initiation factor IIA ... , 2種, 2分子 UV
+Transcription initiation factor IIE subunit ... , 2種, 2分子 WX
+非ポリマー , 5種, 22分子
+詳細
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA タイプ: COMPLEX / Entity ID: #1-#30 / 由来: MULTIPLE SOURCES |
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分子量 | 値: 1.37 MDa / 実験値: NO |
緩衝液 | pH: 7.6 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: COPPER / グリッドのタイプ: Quantifoil R3.5/1 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 130000 X / 最大 デフォーカス(公称値): 4000 nm / 最小 デフォーカス(公称値): 500 nm / アライメント法: ZEMLIN TABLEAU |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 平均露光時間: 9 sec. / 電子線照射量: 43.6 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 実像数: 29670 |
電子光学装置 | エネルギーフィルター名称: GIF Quantum LS / エネルギーフィルタースリット幅: 20 eV |
画像スキャン | 動画フレーム数/画像: 40 |
-解析
ソフトウェア |
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 4300000 | |||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 23887 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: REAL | |||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 5OQJ Accession code: 5OQJ / Source name: PDB / タイプ: experimental model | |||||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 77.45 Å2 | |||||||||||||||||||||||||||
拘束条件 |
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