+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0031 | |||||||||||||||
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タイトル | Structure of activated transcription complex Pol II-DSIF-PAF-SPT6 (Map A) | |||||||||||||||
マップデータ | Postprocessed map of overall refinement with an applied B factor of -98.65(Map A). | |||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 blastocyst growth / inner cell mass cell differentiation / Ski complex / mRNA decay by 3' to 5' exoribonuclease / RNA polymerase II C-terminal domain phosphoserine binding / negative regulation of DNA-templated transcription, elongation / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / regulation of isotype switching / regulation of muscle cell differentiation ...blastocyst growth / inner cell mass cell differentiation / Ski complex / mRNA decay by 3' to 5' exoribonuclease / RNA polymerase II C-terminal domain phosphoserine binding / negative regulation of DNA-templated transcription, elongation / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / regulation of isotype switching / regulation of muscle cell differentiation / regulation of mRNA export from nucleus / negative regulation of myeloid cell differentiation / endodermal cell fate commitment / : / positive regulation of cell cycle G1/S phase transition / DSIF complex / blastocyst hatching / trophectodermal cell differentiation / regulation of mRNA processing / regulation of transcription elongation by RNA polymerase II / nucleosome organization / 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 / 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 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / blastocyst formation / mRNA 3'-end processing / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / stem cell population maintenance / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / interleukin-6-mediated signaling pathway / organelle membrane / mRNA Capping / negative regulation of gene expression, epigenetic / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cell surface receptor signaling pathway via JAK-STAT / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / protein localization to nucleus / mRNA transport / transcription-coupled nucleotide-excision repair / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / nucleosome binding / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / core promoter sequence-specific DNA binding / RNA Polymerase II Pre-transcription Events / translation initiation factor binding / SH2 domain binding / rescue of stalled ribosome / RNA splicing / transcription elongation factor complex / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II 類似検索 - 分子機能 | |||||||||||||||
生物種 | Sus scrofa (ブタ) / Homo sapiens (ヒト) / synthetic construct (人工物) / Pig (ブタ) | |||||||||||||||
手法 | 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 | Vos SM / Farnung L / Boehing M / Linden A / Wigge C / Urlaub H / Cramer P | |||||||||||||||
資金援助 | ドイツ, 4件
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引用 | ジャーナル: Nature / 年: 2018 タイトル: Structure of activated transcription complex Pol II-DSIF-PAF-SPT6. 著者: Seychelle M Vos / Lucas Farnung / Marc Boehning / Christoph Wigge / Andreas Linden / Henning Urlaub / Patrick Cramer / 要旨: Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here ...Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we show that formation of an activated Pol II elongation complex in vitro requires the kinase function of the positive transcription elongation factor b (P-TEFb) and the elongation factors PAF1 complex (PAF) and SPT6. The cryo-EM structure of an activated elongation complex of Sus scrofa Pol II and Homo sapiens DSIF, PAF and SPT6 was determined at 3.1 Å resolution and compared to the structure of the paused elongation complex formed by Pol II, DSIF and NELF. PAF displaces NELF from the Pol II funnel for pause release. P-TEFb phosphorylates the Pol II linker to the C-terminal domain. SPT6 binds to the phosphorylated C-terminal-domain linker and opens the RNA clamp formed by DSIF. These results provide the molecular basis for Pol II pause release and elongation activation. | |||||||||||||||
履歴 |
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-構造の表示
構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
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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_0031.map.gz | 15.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0031-v30.xml emd-0031.xml | 53.9 KB 53.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_0031_fsc_1.xml emd_0031_fsc_2.xml | 12.8 KB 12.8 KB | 表示 表示 | FSCデータファイル |
画像 | emd_0031.png | 78.8 KB | ||
マスクデータ | emd_0031_msk_1.map | 178 MB | マスクマップ | |
その他 | emd_0031_additional.map.gz emd_0031_half_map_1.map.gz emd_0031_half_map_2.map.gz | 140.4 MB 140.9 MB 140.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0031 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0031 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0031_validation.pdf.gz | 395.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0031_full_validation.pdf.gz | 394.4 KB | 表示 | |
XML形式データ | emd_0031_validation.xml.gz | 13.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0031 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0031 | 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_0031.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Postprocessed map of overall refinement with an applied B factor of -98.65(Map A). | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.049 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
-マスク #1
ファイル | emd_0031_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Global refinement of all EC* particles.
ファイル | emd_0031_additional.map | ||||||||||||
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注釈 | Global refinement of all EC* particles. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 1 of global refinement (Map A).
ファイル | emd_0031_half_map_1.map | ||||||||||||
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注釈 | Half map 1 of global refinement (Map A). | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 2 of global refinement (Map A).
ファイル | emd_0031_half_map_2.map | ||||||||||||
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注釈 | Half map 2 of global refinement (Map A). | ||||||||||||
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-DSIF-PAF-SPT6 elongation complex (EC*)
+超分子 #1: RNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*)
+超分子 #2: RNA Polymerase II
+超分子 #3: associated proteins
+超分子 #4: Nucleic acids
+分子 #1: RPB1
+分子 #2: DNA-directed RNA polymerase subunit beta
+分子 #3: RNA polymerase II subunit C
+分子 #4: RNA polymerase II subunit D
+分子 #5: RNA polymerase II subunit E
+分子 #6: RNA polymerase II subunit F
+分子 #7: RNA polymerase II subunit G
+分子 #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #9: DNA-directed RNA polymerase II subunit RPB9
+分子 #10: RPB10
+分子 #11: RPB11
+分子 #12: RPB12
+分子 #13: Transcription elongation factor SPT6,Transcription elongation fac...
+分子 #16: CTR9,RNA polymerase-associated protein CTR9 homolog,RNA polymeras...
+分子 #18: LEO1,LEO1,RNA polymerase-associated protein LEO1
+分子 #19: PAF1,RNA polymerase II-associated factor 1 homolog,RNA polymerase...
+分子 #20: WD repeat-containing protein 61
+分子 #21: CDC73
+分子 #22: Transcription elongation factor SPT4
+分子 #23: Transcription elongation factor SPT5
+分子 #14: Non-template DNA
+分子 #17: Template DNA
+分子 #15: RNA
+分子 #24: ZINC ION
+分子 #25: 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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グリッド | モデル: Quantifoil UltrAuFoil / 材質: GOLD / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV / 詳細: 10s wait prior to blotting, blotting 8.5s. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均露光時間: 10.0 sec. / 平均電子線量: 40.0 e/Å2 |
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: SPOT SCAN / 撮影モード: BRIGHT FIELD / 倍率(公称値): 130000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |