+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-36908 | |||||||||
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タイトル | Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 2 (Pol II Rat1-PTTC2) | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Transcription termination / Pol II / Rat1/Rai1 Spt5 / TRANSCRIPTION (転写 (生物学)) | |||||||||
機能・相同性 | 機能・相同性情報 RNA polymerase II termination complex / negative regulation of transcription elongation by RNA polymerase I / sno(s)RNA processing / positive regulation of termination of RNA polymerase II transcription / positive regulation of transcription elongation by RNA polymerase I / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / termination of RNA polymerase II transcription, poly(A)-coupled / regulation of transcription-coupled nucleotide-excision repair / phosphodiesterase decapping endonuclease activity ...RNA polymerase II termination complex / negative regulation of transcription elongation by RNA polymerase I / sno(s)RNA processing / positive regulation of termination of RNA polymerase II transcription / positive regulation of transcription elongation by RNA polymerase I / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / termination of RNA polymerase II transcription, poly(A)-coupled / regulation of transcription-coupled nucleotide-excision repair / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / termination of RNA polymerase II transcription, exosome-dependent / mRNA 5'-diphosphatase activity / nuclear polyadenylation-dependent rRNA catabolic process / NAD-cap decapping / 5'-3' RNA exonuclease activity / snRNP binding / regulation of rRNA processing / RNA polymerase I core binding / nucleic acid metabolic process / intracellular mRNA localization / DSIF complex / nuclear mRNA surveillance / RNA polymerase I general transcription initiation factor binding / RPB4-RPB7 complex / U4 snRNA binding / : / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / RNA Polymerase I Transcription Initiation / : / transcription elongation-coupled chromatin remodeling / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase II transcription / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / spliceosomal complex assembly / 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 / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerase II complex binding / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / negative regulation of transcription elongation by RNA polymerase II / tRNA transcription by RNA polymerase III / 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 elongation by RNA polymerase I / positive regulation of translational initiation / 加水分解酵素; 酸無水物に作用; リン含有酸無水物に作用 / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / U5 snRNA binding / DNA修復 / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / U2 snRNA binding / U6 snRNA binding / enzyme regulator activity / RNA polymerase II, core complex / positive regulation of autophagy / translation initiation factor binding / U1 snRNA binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / positive regulation of transcription elongation by RNA polymerase II / ribonucleoside binding / 転写後修飾 / rRNA processing / DNA-directed 5'-3' RNA polymerase activity / ポリメラーゼ / cytoplasmic stress granule / ペルオキシソーム / single-stranded DNA binding / リボソーム生合成 / 染色体 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae S288C (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: 2.8 Å | |||||||||
データ登録者 | Zeng Y / Zhang Y | |||||||||
資金援助 | 中国, 2件
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引用 | ジャーナル: Nature / 年: 2024 タイトル: Structural basis of exoribonuclease-mediated mRNA transcription termination. 著者: Yuan Zeng / Hong-Wei Zhang / Xiao-Xian Wu / Yu Zhang / 要旨: Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II ...Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II (Pol II). Here we report two cryogenic electron microscopy structures of Saccharomyces cerevisiae Pol II pre-termination transcription complexes bound to the 5'-to-3' exoribonuclease Rat1 and its partner Rai1. Our structures show that Rat1 displaces the elongation factor Spt5 to dock at the Pol II stalk domain. Rat1 shields the RNA exit channel of Pol II, guides the nascent RNA towards its active centre and stacks three nucleotides at the 5' terminus of the nascent RNA. The structures further show that Rat1 rotates towards Pol II as it shortens RNA. Our results provide the structural mechanism for the Rat1-mediated termination of mRNA transcription by Pol II in yeast and the exoribonuclease-mediated termination of mRNA transcription in other eukaryotes. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_36908.map.gz | 123.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-36908-v30.xml emd-36908.xml | 39 KB 39 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_36908_fsc.xml | 13.1 KB | 表示 | FSCデータファイル |
画像 | emd_36908.png | 127.2 KB | ||
Filedesc metadata | emd-36908.cif.gz | 11.4 KB | ||
その他 | emd_36908_additional_1.map.gz emd_36908_half_map_1.map.gz emd_36908_half_map_2.map.gz | 117.3 MB 226.3 MB 226.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-36908 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36908 | HTTPS FTP |
-関連構造データ
関連構造データ | 8k5pMC 8jchC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_36908.map.gz / 形式: CCP4 / 大きさ: 244.1 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: 1.1 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: #1
ファイル | emd_36908_additional_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_36908_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_36908_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : RNA Polymerase II pre-termination complex bound with Rat1-Rai1 an...
+超分子 #1: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 an...
+分子 #1: DNA-directed RNA polymerase II subunit RPB1
+分子 #2: DNA-directed RNA polymerase II subunit RPB2
+分子 #3: DNA-directed RNA polymerase II subunit RPB3
+分子 #4: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+分子 #5: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #6: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #7: DNA-directed RNA polymerase II subunit RPB9
+分子 #8: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #9: DNA-directed RNA polymerase II subunit RPB11
+分子 #10: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+分子 #14: Transcription elongation factor SPT5
+分子 #15: DNA-directed RNA polymerase II subunit RPB4
+分子 #16: DNA-directed RNA polymerase II subunit RPB7
+分子 #17: 5'-3' exoribonuclease 2
+分子 #18: Decapping nuclease RAI1
+分子 #11: DNA (38-MER)
+分子 #13: DNA (38-MER)
+分子 #12: RNA
+分子 #19: ZINC ION
+分子 #20: MAGNESIUM ION
-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
緩衝液 | pH: 7.4 |
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凍結 | 凍結剤: ETHANE |
-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: DARK FIELD / Cs: 0.01 mm / 最大 デフォーカス(公称値): 1.8 µm / 最小 デフォーカス(公称値): 1.0 µm |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 50.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |