+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-26620 | |||||||||
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タイトル | Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome | |||||||||
マップデータ | Map E, 54 complex, composite | |||||||||
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 / Cdc73/Paf1 complex / regulation of isotype switching ...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 / Cdc73/Paf1 complex / regulation of isotype switching / regulation of mRNA export from nucleus / regulation of muscle cell differentiation / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / blastocyst hatching / DSIF complex / positive regulation of cell cycle G1/S phase transition / nucleosome organization / trophectodermal cell differentiation / regulation of mRNA processing / regulation of transcription elongation by RNA polymerase II / nuclear lumen / mRNA 3'-end processing / 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 / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / transcription elongation-coupled chromatin remodeling / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of gene expression, epigenetic / 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 / : / : / RNA polymerase II complex binding / organelle membrane / cell surface receptor signaling pathway via JAK-STAT / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of macroautophagy / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / transcription factor TFIID complex / protein localization to nucleus / tRNA transcription by RNA polymerase III / positive regulation of Wnt signaling pathway / RNA polymerase III activity / RNA polymerase I activity / 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 / RNA polymerase II activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / nucleosome binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of fibroblast proliferation / DNA-directed RNA polymerase complex / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / rescue of stalled ribosome / SH2 domain binding 類似検索 - 分子機能 | |||||||||
生物種 | pig (ブタ) / Sus scrofa (ブタ) / Homo sapiens (ヒト) / Xenopus laevis (アフリカツメガエル) / 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: 3.0 Å | |||||||||
データ登録者 | Filipovski M / Vos SM / Farnung L | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Science / 年: 2022 タイトル: Structural basis of nucleosome retention during transcription elongation. 著者: Martin Filipovski / Jelly H M Soffers / Seychelle M Vos / Lucas Farnung / 要旨: In eukaryotes, RNA polymerase (Pol) II transcribes chromatin and must move past nucleosomes, often resulting in nucleosome displacement. How Pol II unwraps the DNA from nucleosomes to allow ...In eukaryotes, RNA polymerase (Pol) II transcribes chromatin and must move past nucleosomes, often resulting in nucleosome displacement. How Pol II unwraps the DNA from nucleosomes to allow transcription and how DNA rewraps to retain nucleosomes has been unclear. Here, we report the 3.0-angstrom cryo-electron microscopy structure of a mammalian Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex stalled 54 base pairs within the nucleosome. The structure provides a mechanistic basis for nucleosome retention during transcription elongation where upstream DNA emerging from the Pol II cleft has rewrapped the proximal side of the nucleosome. The structure uncovers a direct role for Pol II and transcription elongation factors in nucleosome retention and explains how nucleosomes are retained to prevent the disruption of chromatin structure across actively transcribed genes. | |||||||||
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_26620.map.gz | 204.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-26620-v30.xml emd-26620.xml | 82.2 KB 82.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_26620.png | 158.2 KB | ||
マスクデータ | emd_26620_msk_1.map emd_26620_msk_2.map emd_26620_msk_3.map | 347.6 MB 347.6 MB 347.6 MB | マスクマップ | |
その他 | emd_26620_additional_1.map.gz emd_26620_additional_10.map.gz emd_26620_additional_11.map.gz emd_26620_additional_12.map.gz emd_26620_additional_13.map.gz emd_26620_additional_14.map.gz emd_26620_additional_15.map.gz emd_26620_additional_16.map.gz emd_26620_additional_2.map.gz emd_26620_additional_3.map.gz emd_26620_additional_4.map.gz emd_26620_additional_5.map.gz emd_26620_additional_6.map.gz emd_26620_additional_7.map.gz emd_26620_additional_8.map.gz emd_26620_additional_9.map.gz | 172.8 MB 327.4 MB 328.6 MB 169 MB 328.3 MB 323 MB 322.3 MB 173.7 MB 173.8 MB 322.3 MB 323 MB 328.2 MB 322.7 MB 322.7 MB 322.2 MB 322.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-26620 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26620 | HTTPS FTP |
-関連構造データ
関連構造データ | 7uncMC 7undC 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_26620.map.gz / 形式: CCP4 / 大きさ: 347.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Map E, 54 complex, composite | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.83 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
+マスク #2
+マスク #3
+追加マップ: Map C, 54 complex, nucleosome local refinement, consensus
+追加マップ: Map D, 54 complex, CTR9/WDR61 local refinement, sharp
+追加マップ: Map A, 54 complex, overall, sharp
+追加マップ: Map D, 54 complex, CTR9/WDR61 local refinement, consensus
+追加マップ: Map B, 54 complex, Pol II (active site) local refinement, sharp
+追加マップ: Map B, 54 complex, Pol II (active site) local refinement, half A
+追加マップ: Map A, 54 complex, overall, half B
+追加マップ: Map A, 54 complex, overall, consensus
+追加マップ: Map B, 54 complex, Pol II local refinement, consensus
+追加マップ: Map A, 54 complex, overall, half A
+追加マップ: Map B, 54 complex, Pol II local refinement, half B
+追加マップ: Map C, 54 complex, nucleosome local refinement, sharp
+追加マップ: Map D, 54 complex, CTR9/WDR61 local refinement, half A
+追加マップ: Map D, 54 complex, CTR9/WDR61 local refinement, half B
+追加マップ: Map C, 54 complex, nucleosome local refinement, half B
+追加マップ: Map C, 54 complex, nucleosome local refinement, half A
-試料の構成要素
+全体 : Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome
+超分子 #1: Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome
+分子 #1: DNA-directed RNA polymerase subunit
+分子 #2: DNA-directed RNA polymerase subunit beta
+分子 #3: DNA-directed RNA polymerase II subunit RPB3
+分子 #4: RPOL4c domain-containing protein
+分子 #5: DNA-directed RNA polymerase II subunit E
+分子 #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #7: DNA-directed RNA polymerase II subunit RPB7
+分子 #8: RPB8
+分子 #9: RPB9
+分子 #10: RPB10
+分子 #11: RPB11
+分子 #12: RNA polymerase II subunit K
+分子 #13: Transcription elongation factor SPT6
+分子 #15: Transcription elongation factor A protein 1
+分子 #17: RNA polymerase-associated protein CTR9 homolog
+分子 #18: RNA polymerase-associated protein RTF1 homolog
+分子 #20: RNA polymerase-associated protein LEO1
+分子 #21: RNA polymerase II-associated factor 1 homolog
+分子 #22: WDR61
+分子 #23: Parafibromin
+分子 #24: Transcription elongation factor SPT5
+分子 #25: Histone H3.2
+分子 #26: Histone H4
+分子 #27: Histone H2A
+分子 #28: Histone H2B 1.1
+分子 #14: Non-template DNA
+分子 #19: Template DNA
+分子 #16: RNA
+分子 #29: ZINC ION
+分子 #30: 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: Quantifoil R2/1 / 材質: COPPER / メッシュ: 200 / 前処理 - タイプ: GLOW DISCHARGE / 詳細: 15 mA with 10 s hold time | ||||||||||||||||||
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 / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 105000 |
特殊光学系 | 位相板: VOLTA PHASE PLATE / 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 K3 BIOQUANTUM (6k x 4k) 平均電子線量: 52.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: OTHER / 詳細: Ab initio |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 使用したクラス数: 1 / 解像度のタイプ: BY AUTHOR / 解像度: 3.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 105420 |