+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0038 | ||||||||||||
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タイトル | Structure of paused transcription complex Pol II-DSIF-NELF | ||||||||||||
マップデータ | Globally refined overall PEC map (Map 1). | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 NELF complex / positive regulation of protein modification process / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation / DSIF complex / 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 ...NELF complex / positive regulation of protein modification process / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation / DSIF complex / 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 / 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 / negative regulation of stem cell differentiation / : / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / transcription elongation-coupled chromatin remodeling / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / mRNA Capping / 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 / positive regulation of translational initiation / RNA polymerase II activity / positive regulation of macroautophagy / organelle membrane / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / transcription-coupled nucleotide-excision repair / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / localization / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / translation initiation factor binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / core promoter sequence-specific DNA binding / RNA Polymerase II Pre-transcription Events / P-body / 細胞分化 / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / ユークロマチン / ribonucleoside binding / 核小体 / DNA-directed 5'-3' RNA polymerase activity / ポリメラーゼ / single-stranded DNA binding / chromatin organization / cell population proliferation / transcription by RNA polymerase II / single-stranded RNA binding / chromosome, telomeric region / nucleic acid binding / positive regulation of ERK1 and ERK2 cascade / protein dimerization activity / molecular adaptor activity / nuclear body / nuclear speck / protein heterodimerization activity / nucleotide binding / mRNA binding / DNA-templated transcription / chromatin binding 類似検索 - 分子機能 | ||||||||||||
生物種 | Sus scrofa (ブタ) / Homo sapiens (ヒト) / Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) / 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: 3.2 Å | ||||||||||||
データ登録者 | Vos SM / Farnung L / Urlaub H / Cramer P | ||||||||||||
資金援助 | ドイツ, 3件
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引用 | ジャーナル: Nature / 年: 2018 タイトル: Structure of paused transcription complex Pol II-DSIF-NELF. 著者: Seychelle M Vos / Lucas Farnung / Henning Urlaub / Patrick Cramer / 要旨: Metazoan gene regulation often involves the pausing of RNA polymerase II (Pol II) in the promoter-proximal region. Paused Pol II is stabilized by the protein complexes DRB sensitivity-inducing factor ...Metazoan gene regulation often involves the pausing of RNA polymerase II (Pol II) in the promoter-proximal region. Paused Pol II is stabilized by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we report the cryo-electron microscopy structure of a paused transcription elongation complex containing Sus scrofa Pol II and Homo sapiens DSIF and NELF at 3.2 Å resolution. The structure reveals a tilted DNA-RNA hybrid that impairs binding of the nucleoside triphosphate substrate. NELF binds the polymerase funnel, bridges two mobile polymerase modules, and contacts the trigger loop, thereby restraining Pol II mobility that is required for pause release. NELF prevents binding of the anti-pausing transcription elongation factor IIS (TFIIS). Additionally, NELF possesses two flexible 'tentacles' that can contact DSIF and exiting RNA. These results define the paused state of Pol II and provide the molecular basis for understanding the function of NELF during promoter-proximal gene regulation. | ||||||||||||
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_0038.map.gz | 49.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0038-v30.xml emd-0038.xml | 48 KB 48 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_0038_fsc.xml | 9.1 KB | 表示 | FSCデータファイル |
画像 | emd_0038.png | 192.2 KB | ||
マスクデータ | emd_0038_msk_1.map | 64 MB | マスクマップ | |
その他 | emd_0038_additional.map.gz emd_0038_half_map_1.map.gz emd_0038_half_map_2.map.gz | 7.7 MB 49.6 MB 49.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0038 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0038 | 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_0038.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Globally refined overall PEC map (Map 1). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.2277 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_0038_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: Postprocessed/B-factor sharpened overall PEC map (Map 1). Applied...
ファイル | emd_0038_additional.map | ||||||||||||
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注釈 | Postprocessed/B-factor sharpened overall PEC map (Map 1). Applied B-factor of -65. | ||||||||||||
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 for globally refined PEC (Map 1).
ファイル | emd_0038_half_map_1.map | ||||||||||||
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注釈 | Half map 1 for globally refined PEC (Map 1). | ||||||||||||
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 for globally refined PEC (Map 1).
ファイル | emd_0038_half_map_2.map | ||||||||||||
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注釈 | Half map 2 for globally refined PEC (Map 1). | ||||||||||||
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 elongation complex bound to DSIF and NELF
+超分子 #1: RNA Polymerase II elongation complex bound to DSIF and NELF
+超分子 #2: Sus scrofa RNA Polymerase II
+超分子 #3: Negative elongation factor (NELF)
+超分子 #4: DRB sensitivity inducing factor (DSIF)
+超分子 #5: HIV-1 pause transcription scaffold
+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 E
+分子 #5: RNA polymerase II subunit F
+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: Uncharacterized protein
+分子 #9: Uncharacterized protein
+分子 #10: Uncharacterized protein
+分子 #14: Negative elongation factor A
+分子 #15: Negative elongation factor B,Negative elongation factor B
+分子 #16: Negative elongation factor C/D
+分子 #17: Negative elongation factor E,Negative elongation factor E
+分子 #18: Transcription elongation factor SPT4
+分子 #19: Transcription elongation factor SPT5
+分子 #20: RNA polymerase II subunit D
+分子 #21: RNA polymerase II subunit G
+分子 #11: Non-template DNA
+分子 #13: Template DNA
+分子 #12: TAR RNA
+分子 #22: MAGNESIUM ION
+分子 #23: ZINC 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
濃度 | 0.2 mg/mL |
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緩衝液 | pH: 7.4 |
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 |
-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: SPOT SCAN / 撮影モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 165000 |
特殊光学系 | エネルギーフィルター - 名称: GIF Quantum LS / エネルギーフィルター - スリット幅: 20 eV |
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 |
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 / 実像数: 11740 / 平均露光時間: 9.0 sec. / 平均電子線量: 46.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |