+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8134 | |||||||||||||||
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タイトル | Human holo-PIC in the initial transcribing state (no IIS) | |||||||||||||||
マップデータ | None | |||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 LRR domain binding / microfibril binding / RNA Polymerase III Chain Elongation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / RNA Polymerase III Transcription Termination / positive regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation ...LRR domain binding / microfibril binding / RNA Polymerase III Chain Elongation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / RNA Polymerase III Transcription Termination / positive regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / positive regulation of core promoter binding / RPAP3/R2TP/prefoldin-like complex / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / hair follicle maturation / hair cell differentiation / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / regulation of transcription by RNA polymerase I / 紫外線 / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / RNA polymerase transcription factor SL1 complex / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase I core promoter sequence-specific DNA binding / 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 / G protein-coupled receptor internalization / female germ cell nucleus / male pronucleus / transcription factor TFIIH core complex / female pronucleus / transcription factor TFIIH holo complex / 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 / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / Signaling by FGFR2 IIIa TM / 3'-5' DNA helicase activity / spinal cord development / 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 / protein acetylation / PIWI-interacting RNA (piRNA) biogenesis / : / : / cell division site / bone mineralization / 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 / RNA polymerase II complex binding / mRNA Splicing - Minor Pathway / erythrocyte maturation / ATPase activator activity / viral transcription / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / acetyltransferase activity / RNA Polymerase I Transcription Initiation / transcription elongation by RNA polymerase I / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / DNA topological change / aryl hydrocarbon receptor binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / transcription factor TFIID complex / TFIIB-class transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / RNA polymerase II general transcription initiation factor activity / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I 類似検索 - 分子機能 | |||||||||||||||
生物種 | Homo sapiens (ヒト) / Human (ヒト) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.3 Å | |||||||||||||||
データ登録者 | He Y / Yan C / Fang J / Inouye C / Tjian R / Ivanov I / Nogales E | |||||||||||||||
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_8134.map.gz | 1.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-8134-v30.xml emd-8134.xml | 52.2 KB 52.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_8134_fsc.xml | 6.9 KB | 表示 | FSCデータファイル |
画像 | emd_8134.png | 151.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8134 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8134 | HTTPS FTP |
-関連構造データ
関連構造データ | 5iy9MC 8131C 8132C 8133C 8135C 8136C 8137C 8138C 5ivwC 5iy6C 5iy7C 5iy8C 5iyaC 5iybC 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_8134.map.gz / 形式: CCP4 / 大きさ: 27 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: 2.62 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 holo-PIC in the initial transcribing state (no IIS)
+超分子 #1: Human holo-PIC in the initial transcribing state (no IIS)
+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: TFIIH basal transcription factor complex helicase XPB subunit
+分子 #22: TFIIH basal transcription factor complex helicase XPD subunit
+分子 #23: General transcription factor IIH subunit 2
+分子 #24: General transcription factor IIH subunit 5
+分子 #25: General transcription factor IIH subunit 4
+分子 #26: General transcription factor IIH subunit 3
+分子 #27: SCP-X
+分子 #28: SCP-Y
+分子 #29: RNA
+分子 #30: MAGNESIUM ION
+分子 #31: 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-5iy9: |