+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8rbx | ||||||||||||
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タイトル | Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex | ||||||||||||
要素 |
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キーワード | TRANSCRIPTION (転写 (生物学)) / Integrator complex (積分器) / Pre-termination complex | ||||||||||||
機能・相同性 | 機能・相同性情報 regulation of fertilization / U2 snRNA 3'-end processing / NELF complex / positive regulation of protein modification process / snRNA processing / integrator complex / snRNA 3'-end processing / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors ...regulation of fertilization / U2 snRNA 3'-end processing / NELF complex / positive regulation of protein modification process / snRNA processing / integrator complex / snRNA 3'-end processing / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / regulation of meiotic cell cycle process involved in oocyte maturation / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / flagellated sperm motility / peptidyl-serine dephosphorylation / DSIF complex / protein localization to nuclear envelope / regulation of transcription elongation by RNA polymerase II / peptidyl-threonine dephosphorylation / : / positive regulation of microtubule binding / negative regulation of tyrosine phosphorylation of STAT protein / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein antigen binding / protein phosphatase regulator activity / ceramide metabolic process / GABA receptor binding / negative regulation of epithelial to mesenchymal transition / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Initiation of Nuclear Envelope (NE) Reformation / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / ERKs are inactivated / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / negative regulation of stem cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / 加水分解酵素; エステル加水分解酵素; 3'-リン酸モノエステル産生エンドリボヌクレアーゼ / nuclear lumen / Abortive elongation of HIV-1 transcript in the absence of Tat / regulation of Wnt signaling pathway / positive regulation of DNA-templated transcription, elongation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of growth / nucleosomal DNA binding / centrosome localization / : / transcription elongation-coupled chromatin remodeling / inner cell mass cell proliferation / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / myosin phosphatase activity / protein serine/threonine phosphatase activity / CTLA4 inhibitory signaling / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Platelet sensitization by LDL / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / negative regulation of MAPK cascade 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) Sus scrofa (ブタ) Trichoplusia ni (イラクサキンウワバ) synthetic construct (人工物) | ||||||||||||
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: 4.1 Å | ||||||||||||
データ登録者 | Fianu, I. / Ochmann, M. / Walshe, J.L. / Cramer, P. | ||||||||||||
資金援助 | ドイツ, European Union, 3件
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引用 | ジャーナル: Nature / 年: 2024 タイトル: Structural basis of Integrator-dependent RNA polymerase II termination. 著者: Isaac Fianu / Moritz Ochmann / James L Walshe / Olexandr Dybkov / Joseph Neos Cruz / Henning Urlaub / Patrick Cramer / 要旨: The Integrator complex can terminate RNA polymerase II (Pol II) in the promoter-proximal region of genes. Previous work has shed light on how Integrator binds to the paused elongation complex ...The Integrator complex can terminate RNA polymerase II (Pol II) in the promoter-proximal region of genes. Previous work has shed light on how Integrator binds to the paused elongation complex consisting of Pol II, the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) and how it cleaves the nascent RNA transcript, but has not explained how Integrator removes Pol II from the DNA template. Here we present three cryo-electron microscopy structures of the complete Integrator-PP2A complex in different functional states. The structure of the pre-termination complex reveals a previously unresolved, scorpion-tail-shaped INTS10-INTS13-INTS14-INTS15 module that may use its 'sting' to open the DSIF DNA clamp and facilitate termination. The structure of the post-termination complex shows that the previously unresolved subunit INTS3 and associated sensor of single-stranded DNA complex (SOSS) factors prevent Pol II rebinding to Integrator after termination. The structure of the free Integrator-PP2A complex in an inactive closed conformation reveals that INTS6 blocks the PP2A phosphatase active site. These results lead to a model for how Integrator terminates Pol II transcription in three steps that involve major rearrangements. | ||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8rbx.cif.gz | 3 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8rbx.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 8rbx.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/rb/8rbx ftp://data.pdbj.org/pub/pdb/validation_reports/rb/8rbx | HTTPS FTP |
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-関連構造データ
関連構造データ | 19038MC 8rbzC 8rc4C 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 | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
+UNK-UNK-UNK-UNK-UNK-UNK-UNK- ... , 2種, 2分子 1x
+DNA-directed RNA polymerase ... , 7種, 8分子 AYBCEGIK
+RNA polymerase II subunit ... , 2種, 2分子 DL
+DNA-directed RNA polymerases I, II, and III subunit ... , 3種, 3分子 FHJ
+タンパク質 , 6種, 10分子 MSOUQVRWZv
+DNA鎖 , 2種, 2分子 NT
+Integrator complex subunit ... , 13種, 13分子 abdefghijkmno
+Serine/threonine-protein phosphatase 2A ... , 2種, 2分子 pq
+Negative elongation factor ... , 2種, 2分子 uw
+RNA鎖 / タンパク質・ペプチド , 2種, 2分子 Pr
+非ポリマー , 3種, 13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 | 値: 1.8 MDa / 実験値: NO | |||||||||||||||||||||||||||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||
試料 | 濃度: 0.3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||||||||||||||||||||||||||||||||||||
試料支持 | グリッドのタイプ: Qu | |||||||||||||||||||||||||||||||||||||||||||||||||
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: OTHER |
電子レンズ | モード: OTHER / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 500 nm |
撮影 | 電子線照射量: 40.44 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
EMソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / カテゴリ: モデル精密化 | |||||||||||||||||||||||||||||||||||
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CTF補正 | タイプ: NONE | |||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 80717 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||
原子モデル構築 |
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原子モデル構築 |
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