+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-15006 | |||||||||||||||
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タイトル | Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC) | |||||||||||||||
マップデータ | ||||||||||||||||
試料 |
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キーワード | RNA polymerase II / Pol II / PIC / SNAPc / snRNA / U1 promoter / TRANSCRIPTION | |||||||||||||||
機能・相同性 | 機能・相同性情報 snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / : / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / snRNA transcription by RNA polymerase II ...snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / : / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / snRNA transcription by RNA polymerase II / RNA polymerase transcription factor SL1 complex / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / TFIIF-class transcription factor complex binding / 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 / RNA polymerase I core promoter sequence-specific DNA binding / transcriptional start site selection at RNA polymerase II promoter / 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 / transcription factor TFIIF complex / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / germinal vesicle / transcription preinitiation complex / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / organelle membrane / mRNA Capping / cell division site / protein acetylation / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / mRNA Splicing - Minor Pathway / acetyltransferase activity / RNA Polymerase I Transcription Initiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / viral transcription / aryl hydrocarbon receptor binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Processing of Capped Intron-Containing Pre-mRNA / transcription by RNA polymerase III / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / TFIIB-class transcription factor binding / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / Tat-mediated elongation of the HIV-1 transcript 類似検索 - 分子機能 | |||||||||||||||
生物種 | Homo sapiens (ヒト) / Sus scrofa (ブタ) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | |||||||||||||||
データ登録者 | Rengachari S / Schilbach S / Kaliyappan T / Gouge J / Zumer K / Schwarz J / Urlaub H / Dienemann C / Vannini A / Cramer P | |||||||||||||||
資金援助 | ドイツ, 英国, 4件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2022 タイトル: Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II. 著者: Srinivasan Rengachari / Sandra Schilbach / Thangavelu Kaliyappan / Jerome Gouge / Kristina Zumer / Juliane Schwarz / Henning Urlaub / Christian Dienemann / Alessandro Vannini / Patrick Cramer / 要旨: RNA polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at ...RNA polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at non-coding genes, such as small nuclear RNA (snRNA) genes, is less well understood at the structural level. Here, we study Pol II initiation at snRNA gene promoters and show that the snRNA-activating protein complex (SNAPc) enables DNA opening and transcription initiation independent of TFIIE and TFIIH in vitro. We then resolve cryo-EM structures of the SNAPc-containing Pol IIpre-initiation complex (PIC) assembled on U1 and U5 snRNA promoters. The core of SNAPc binds two turns of DNA and recognizes the snRNA promoter-specific proximal sequence element (PSE), located upstream of the TATA box-binding protein TBP. Two extensions of SNAPc, called wing-1 and wing-2, bind TFIIA and TFIIB, respectively, explaining how SNAPc directs Pol II to snRNA promoters. Comparison of structures of closed and open promoter complexes elucidates TFIIH-independent DNA opening. These results provide the structural basis of Pol II initiation at non-coding RNA gene promoters. #1: ジャーナル: Biorxiv / 年: 2022 タイトル: Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II 著者: Rengachari S / Schilbach S / Kaliyappan T / Gouge J / Zumer K / Schwarz J / Urlaub H / Dienemann C / Vannini A / Cramer P | |||||||||||||||
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_15006.map.gz | 141.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-15006-v30.xml emd-15006.xml | 51.3 KB 51.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_15006_fsc.xml | 14.1 KB | 表示 | FSCデータファイル |
画像 | emd_15006.png | 94.1 KB | ||
マスクデータ | emd_15006_msk_1.map | 244.1 MB | マスクマップ | |
Filedesc metadata | emd-15006.cif.gz | 12.9 KB | ||
その他 | emd_15006_half_map_1.map.gz emd_15006_half_map_2.map.gz | 193.9 MB 194.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-15006 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15006 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_15006_validation.pdf.gz | 805.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_15006_full_validation.pdf.gz | 805.3 KB | 表示 | |
XML形式データ | emd_15006_validation.xml.gz | 21.2 KB | 表示 | |
CIF形式データ | emd_15006_validation.cif.gz | 27.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15006 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15006 | 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_15006.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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: 1.05 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_15006_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 |
-ハーフマップ: #2
ファイル | emd_15006_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_15006_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 : Pre-initiation complex of RNA polymerase II with general transcri...
+超分子 #1: Pre-initiation complex of RNA polymerase II with general transcri...
+超分子 #2: SNAPc
+超分子 #3: TATA-box-binding protein and transcription factors
+超分子 #4: Promoter
+超分子 #5: RNA polymerase II
+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 polymerase II subunit F
+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: RNA polymerase II subunit J
+分子 #12: RNA polymerase II subunit K
+分子 #13: Transcription initiation factor IIB
+分子 #15: TATA-box-binding protein
+分子 #16: General transcription factor IIF subunit 1
+分子 #17: General transcription factor IIF subunit 2
+分子 #19: Transcription initiation factor IIA subunit 1
+分子 #20: Transcription initiation factor IIA subunit 2
+分子 #21: snRNA-activating protein complex subunit 1
+分子 #22: snRNA-activating protein complex subunit 3
+分子 #23: snRNA-activating protein complex subunit 4
+分子 #24: snRNA-activating protein complex subunit 5
+分子 #14: Non-template strand
+分子 #18: Template strand
+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: 7.5 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | TFS 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: 54.45 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): 2.5 µm / 最小 デフォーカス(公称値): 0.3 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |