+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8136 | |||||||||||||||
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タイトル | Human core-PIC in the open state | |||||||||||||||
マップデータ | None | |||||||||||||||
試料 |
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キーワード | initiation / RNA polymerase II (RNAポリメラーゼII) / human (ヒト) / TRANSCRIPTION (転写 (生物学)) / TRANSFERASE-DNA complex | |||||||||||||||
機能・相同性 | 機能・相同性情報 LRR domain binding / microfibril binding / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase I / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / RPAP3/R2TP/prefoldin-like complex / RNA polymerase transcription factor SL1 complex ...LRR domain binding / microfibril binding / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase I / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / RPAP3/R2TP/prefoldin-like complex / RNA polymerase transcription factor SL1 complex / transcription factor TFIIE complex / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / Cytosolic sensors of pathogen-associated DNA / 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 / 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 / 卵母細胞 / RNA polymerase II general transcription initiation factor binding / MicroRNA (miRNA) biogenesis / nuclear thyroid hormone receptor binding / 転写開始前複合体 / FGFR2 alternative splicing / RNA Polymerase I Transcription Termination / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / cell division site / 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 / 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 / protein acetylation / RNA polymerase II general transcription initiation factor activity / PIWI-interacting RNA (piRNA) biogenesis / RNA polymerase II complex binding / 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 / mRNA Splicing - Minor Pathway / tRNA transcription by RNA polymerase III / viral transcription / acetyltransferase activity / RNA Polymerase I Transcription Initiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of translational initiation / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / TFIIB-class transcription factor binding / transcription-coupled nucleotide-excision repair / positive regulation of transcription initiation by RNA polymerase II / spindle assembly / RNA polymerase II core promoter sequence-specific DNA binding / Tat-mediated elongation of the HIV-1 transcript / RNA polymerase II activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / 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 preinitiation complex assembly / histone acetyltransferase activity / ヒストンアセチルトランスフェラーゼ / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / TBP-class protein binding / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / SIRT1 negatively regulates rRNA expression / negative regulation of protein binding / male germ cell nucleus 類似検索 - 分子機能 | |||||||||||||||
生物種 | Homo sapiens (ヒト) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||||||||
データ登録者 | He Y / Yan C | |||||||||||||||
資金援助 | 米国, 4件
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引用 | ジャーナル: Nature / 年: 2016 タイトル: Near-atomic resolution visualization of human transcription promoter opening. 著者: Yuan He / Chunli Yan / Jie Fang / Carla Inouye / Robert Tjian / Ivaylo Ivanov / Eva Nogales / 要旨: In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the ...In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA-RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB. | |||||||||||||||
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_8136.map.gz | 4.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-8136-v30.xml emd-8136.xml | 46.3 KB 46.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_8136_fsc.xml | 13.6 KB | 表示 | FSCデータファイル |
画像 | emd_8136.png | 161.9 KB | ||
Filedesc metadata | emd-8136.cif.gz | 12.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8136 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8136 | HTTPS FTP |
-関連構造データ
関連構造データ | 5iybMC 8131C 8132C 8133C 8134C 8135C 8137C 8138C 5ivwC 5iy6C 5iy7C 5iy8C 5iy9C 5iyaC 5iycC 5iydC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ |
-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_8136.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.31 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
-試料の構成要素
+全体 : Human core-PIC in the open state
+超分子 #1: Human core-PIC in the open state
+超分子 #2: RNA polymerase II
+超分子 #3: General transcription factors
+超分子 #4: Super core promoter
+分子 #1: DNA-directed RNA polymerase II subunit RPB1
+分子 #2: DNA-directed RNA polymerase II subunit RPB2
+分子 #3: DNA-directed RNA polymerase II subunit RPB3
+分子 #4: DNA-directed RNA polymerase II subunit RPB4
+分子 #5: DNA-directed RNA polymerase II subunit RPB5
+分子 #6: DNA-directed RNA polymerase II subunit RPB6
+分子 #7: DNA-directed RNA polymerase II subunit RPB7
+分子 #8: DNA-directed RNA polymerase II subunit RPB8
+分子 #9: DNA-directed RNA polymerase II subunit RPB9
+分子 #10: DNA-directed RNA polymerase II subunit RPB10
+分子 #11: DNA-directed RNA polymerase II subunit RPB11-a
+分子 #12: DNA-directed RNA polymerase II subunit RPB12
+分子 #13: Transcription initiation factor IIB
+分子 #14: Transcription initiation factor IIA subunit 1
+分子 #15: Transcription initiation factor IIA subunit 2
+分子 #16: TATA-box-binding protein
+分子 #17: General transcription factor IIE subunit 1
+分子 #18: Transcription initiation factor IIE subunit beta
+分子 #19: General transcription factor IIF subunit 1
+分子 #20: General transcription factor IIF subunit 2
+分子 #21: Transcription elongation factor A protein 1
+分子 #22: SCP-X
+分子 #23: SCP-Y
+分子 #24: MAGNESIUM ION
+分子 #25: 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 | 0.3 mg/mL |
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緩衝液 | pH: 7.9 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK IV 詳細: Blot for 4 seconds before plunging into liquid ethane (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: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス(公称値): 4.0 µm / 最小 デフォーカス(公称値): 2.0 µm / 倍率(公称値): 27500 |
試料ステージ | 試料ホルダーモデル: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 42.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
-原子モデル構築 1
精密化 | プロトコル: FLEXIBLE FIT |
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得られたモデル | PDB-5iyb: |