+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10480 | |||||||||||||||
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タイトル | Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1 (Map 1) | |||||||||||||||
マップデータ | B factor of -115 applied | |||||||||||||||
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 / positive regulation of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / RNA polymerase II C-terminal domain phosphoserine binding / negative regulation of DNA-templated transcription, elongation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / regulation of isotype switching / regulation of mRNA export from nucleus ...blastocyst growth / inner cell mass cell differentiation / Ski complex / positive regulation of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / RNA polymerase II C-terminal domain phosphoserine binding / negative regulation of DNA-templated transcription, elongation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / regulation of isotype switching / regulation of mRNA export from nucleus / regulation of muscle cell differentiation / Cdc73/Paf1 complex / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / blastocyst hatching / DSIF complex / positive regulation of cell cycle G1/S phase transition / trophectodermal cell differentiation / nucleosome organization / regulation of mRNA processing / regulation of transcription elongation by RNA polymerase II / 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 / mRNA 3'-end processing / 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 / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / negative regulation of gene expression, epigenetic / negative regulation of G1/S transition of mitotic cell cycle / stem cell population maintenance / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / interleukin-6-mediated signaling pathway / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / : / : / negative regulation of transcription elongation by RNA polymerase II / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / organelle membrane / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / cell surface receptor signaling pathway via JAK-STAT / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / transcription by RNA polymerase I / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / positive regulation of macroautophagy / protein localization to nucleus / positive regulation of Wnt signaling pathway / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / mRNA transport / positive regulation of translational initiation / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / RNA polymerase II activity / Formation of RNA Pol II elongation complex / negative regulation of fibroblast proliferation / nucleosome binding / translation initiation factor binding / RNA Polymerase II Pre-transcription Events 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 / Cramer P | |||||||||||||||
資金援助 | ドイツ, 4件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2020 タイトル: Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation. 著者: Seychelle M Vos / Lucas Farnung / Andreas Linden / Henning Urlaub / Patrick Cramer / 要旨: Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation ...Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation factors DSIF, PAF1 complex (PAF) and SPT6. Here we report the cryo-EM structure of the complete EC* that contains RTF1, a dissociable PAF subunit critical for chromatin transcription. The RTF1 Plus3 domain associates with Pol II subunit RPB12 and the phosphorylated C-terminal region of DSIF subunit SPT5. RTF1 also forms four α-helices that extend from the Plus3 domain along the Pol II protrusion and RPB10 to the polymerase funnel. The C-terminal 'fastener' helix retains PAF and is followed by a 'latch' that reaches the end of the bridge helix, a flexible element of the Pol II active site. RTF1 strongly stimulates Pol II elongation, and this requires the latch, possibly suggesting that RTF1 activates transcription allosterically by influencing Pol II translocation. | |||||||||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
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_10480.map.gz | 160.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10480-v30.xml emd-10480.xml | 56.6 KB 56.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_10480_fsc.xml | 12.8 KB | 表示 | FSCデータファイル |
画像 | emd_10480.png | 168.3 KB | ||
マスクデータ | emd_10480_msk_1.map emd_10480_msk_2.map | 178 MB 178 MB | マスクマップ | |
その他 | emd_10480_additional.map.gz emd_10480_half_map_1.map.gz emd_10480_half_map_2.map.gz | 158.8 MB 139.7 MB 139.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10480 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10480 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_10480_validation.pdf.gz | 439.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_10480_full_validation.pdf.gz | 438.5 KB | 表示 | |
XML形式データ | emd_10480_validation.xml.gz | 18.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10480 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10480 | 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_10480.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 | B factor of -115 applied | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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:
CCP4マップ ヘッダ情報:
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-添付データ
-マスク #1
ファイル | emd_10480_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 |
-マスク #2
ファイル | emd_10480_msk_2.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: Composite map used for model refinement. Generated using maps 1, 2,
ファイル | emd_10480_additional.map | ||||||||||||
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注釈 | Composite map used for model refinement. Generated using maps 1, 2, | ||||||||||||
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_10480_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: #2
ファイル | emd_10480_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 : Complete EC*
+超分子 #1: Complete EC*
+超分子 #2: Pig DNA/RNA polymerase subunits
+超分子 #3: Human transcription factors and associated proteins
+超分子 #4: DNA/RNA
+超分子 #5: Transcription elongation factor SPT4 and SPT5
+分子 #1: DNA-directed RNA polymerase subunit
+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: Uncharacterized protein
+分子 #11: Uncharacterized protein
+分子 #12: Uncharacterized protein
+分子 #13: Transcription elongation factor SPT6
+分子 #16: RNA polymerase-associated protein CTR9 homolog
+分子 #17: RNA polymerase-associated protein RTF1 homolog
+分子 #19: RNA polymerase-associated protein LEO1
+分子 #20: RNA polymerase II-associated factor 1 homolog
+分子 #21: WD repeat-containing protein 61
+分子 #22: Parafibromin
+分子 #23: Transcription elongation factor SPT4
+分子 #24: Transcription elongation factor SPT5
+分子 #14: DNA (37-MER)
+分子 #18: Template DNA
+分子 #15: RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP...
+分子 #25: ZINC ION
+分子 #26: 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 構成要素:
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グリッド | モデル: 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: 2 microliters applied to both sides of grid. Sample incubated on grid for 10s prior to blotting. Blotting for 8.5s.. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 検出モード: COUNTING / 撮影したグリッド数: 3 / 実像数: 13679 / 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 |