+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7ml4 | ||||||||||||||||||
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タイトル | RNA polymerase II initially transcribing complex (ITC) | ||||||||||||||||||
要素 |
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キーワード | TRANSCRIPTION / PIC / TFIIH / ITC / RNA polymerase II | ||||||||||||||||||
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 / 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 ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / 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 / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 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 / 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 / cyclin-dependent protein serine/threonine kinase activator activity / DNA 3'-5' helicase / DNA duplex unwinding / transcription preinitiation complex / 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 / 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 Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / 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 / RNA polymerase III activity / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / ATPase activator activity / acetyltransferase activity / Dual incision in TC-NER / RNA polymerase II activity / positive regulation of translational initiation / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase II, core complex / RNA polymerase I activity / RNA polymerase II preinitiation complex assembly / DNA helicase activity / translation initiation factor binding / TBP-class protein binding / 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 / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / disordered domain specific binding / single-stranded DNA binding / double-stranded DNA binding / DNA-binding transcription factor binding / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / nucleic acid binding / damaged DNA binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Saccharomyces cerevisiae (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: 3.1 Å | ||||||||||||||||||
データ登録者 | Yang, C. / Fujiwara, R. / Kim, H.J. / Gorbea Colon, J.J. / Steimle, S. / Garcia, B.A. / Murakami, K. | ||||||||||||||||||
資金援助 | 米国, 5件
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引用 | ジャーナル: Mol Cell / 年: 2022 タイトル: Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. 著者: Chun Yang / Rina Fujiwara / Hee Jong Kim / Pratik Basnet / Yunye Zhu / Jose J Gorbea Colón / Stefan Steimle / Benjamin A Garcia / Craig D Kaplan / Kenji Murakami / 要旨: Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous ...Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation. | ||||||||||||||||||
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 | 7ml4.cif.gz | 1.5 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7ml4.ent.gz | 1.2 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7ml4.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 | 7ml4_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7ml4_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | 7ml4_validation.xml.gz | 231.6 KB | 表示 | |
CIF形式データ | 7ml4_validation.cif.gz | 360.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ml/7ml4 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/7ml4 | HTTPS FTP |
-関連構造データ
関連構造データ | 23908MC 7meiC 7mk9C 7mkaC 7ml0C 7ml1C 7ml2C 7ml3C M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10865 (タイトル: Structural visualization of de novo initiation of RNA polymerase II transcription Data size: 14.3 TB Data #1: raw micrographs for PIC + ITC maps [micrographs - multiframe] Data #2: raw micrographs for EC+EC map [micrographs - multiframe]) |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
+Transcription initiation factor IIF subunit ... , 2種, 2分子 QR
+DNA-directed RNA polymerase ... , 7種, 7分子 DGABCIK
+タンパク質 , 7種, 7分子 MF3612O
+DNA-directed RNA polymerases I, II, and III subunit ... , 2種, 2分子 EH
+DNA-directed RNA polymerases II subunit ... , 2種, 2分子 JL
+General transcription and DNA repair factor IIH helicase subunit ... , 2種, 2分子 07
+General transcription and DNA repair factor IIH subunit ... , 2種, 2分子 45
+Transcription initiation factor IIE subunit ... , 2種, 2分子 XW
+Transcription initiation factor IIA ... , 2種, 2分子 UV
+DNA鎖 , 2種, 2分子 NT
+RNA鎖 , 1種, 1分子 P
+非ポリマー , 3種, 17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 |
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分子量 |
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由来(天然) |
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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 | |||||||||||||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE |
-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 / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 500 nm |
撮影 | 電子線照射量: 45 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
3次元再構成 | 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 254448 詳細: final map is a composite of 3 individually refined domains 対称性のタイプ: POINT | ||||||||||||||||||||
原子モデル構築 | 空間: REAL | ||||||||||||||||||||
原子モデル構築 | PDB-ID: 5OQJ |