+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-15129 | ||||||||||||
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タイトル | Structure of mammalian Pol II-TFIIS elongation complex | ||||||||||||
マップデータ | |||||||||||||
試料 |
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キーワード | chromatin / rna polymerase II / nucleosome / TFIIS / transcription / elongation | ||||||||||||
機能・相同性 | 機能・相同性情報 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 ...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 / : / : / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase III activity / organelle membrane / 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 / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / transcription factor TFIID complex / RNA polymerase II activity / Tat-mediated elongation of the HIV-1 transcript / positive regulation of translational initiation / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase II, core complex / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / P-body / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / ribonucleoside binding / Formation of TC-NER Pre-Incision Complex / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / chromosome, telomeric region / single-stranded RNA binding / protein dimerization activity / nuclear speck / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / chromatin binding / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | Sus scrofa (ブタ) / Homo sapiens (ヒト) / 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 | Farnung L / Ochmann M / Garg G / Vos SM / Cramer P | ||||||||||||
資金援助 | European Union, ドイツ, 3件
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引用 | ジャーナル: Mol Cell / 年: 2022 タイトル: Structure of a backtracked hexasomal intermediate of nucleosome transcription. 著者: Lucas Farnung / Moritz Ochmann / Gaurika Garg / Seychelle M Vos / Patrick Cramer / 要旨: During gene transcription, RNA polymerase II (RNA Pol II) passes nucleosomes with the help of various elongation factors. Here, we show that RNA Pol II achieves efficient nucleosome passage when the ...During gene transcription, RNA polymerase II (RNA Pol II) passes nucleosomes with the help of various elongation factors. Here, we show that RNA Pol II achieves efficient nucleosome passage when the human elongation factors DSIF, PAF1 complex (PAF), RTF1, SPT6, and TFIIS are present. The cryo-EM structure of an intermediate of the nucleosome passage shows a partially unraveled hexasome that lacks the proximal H2A-H2B dimer and interacts with the RNA Pol II jaw, DSIF, and the CTR9trestle helix. RNA Pol II adopts a backtracked state with the RNA 3' end dislodged from the active site and bound in the RNA Pol II pore. Additional structures and biochemical data show that human TFIIS enters the RNA Pol II pore and stimulates the cleavage of the backtracked RNA and nucleosome passage. | ||||||||||||
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_15129.map.gz | 80.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-15129-v30.xml emd-15129.xml | 31.6 KB 31.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_15129.png | 109.4 KB | ||
Filedesc metadata | emd-15129.cif.gz | 9.7 KB | ||
その他 | emd_15129_half_map_1.map.gz emd_15129_half_map_2.map.gz | 80.8 MB 80.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-15129 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15129 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_15129_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_15129_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_15129_validation.xml.gz | 13 KB | 表示 | |
CIF形式データ | emd_15129_validation.cif.gz | 14.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15129 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15129 | 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_15129.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 0.834 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
-ハーフマップ: #2
ファイル | emd_15129_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: #1
ファイル | emd_15129_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 : Mammalian Pol II-TFIIS elongation complex
+超分子 #1: Mammalian Pol II-TFIIS elongation complex
+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: RNA polymerase II subunit D
+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: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #9: DNA-directed RNA polymerase II subunit RPB9
+分子 #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #11: DNA-directed RNA polymerase II subunit RPB11-a
+分子 #12: RNA polymerase II subunit K
+分子 #16: Transcription elongation factor A protein 1
+分子 #13: Non-template DNA
+分子 #15: Template DNA
+分子 #14: RNA
+分子 #17: ZINC ION
+分子 #18: 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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凍結 | 凍結剤: ETHANE |
-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 K3 BIOQUANTUM (6k x 4k) 平均電子線量: 50.0 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 1.2 µm |
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 |
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最終 再構成 | 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: 3000 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |