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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-31109 | |||||||||
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タイトル | TFIID-based intermediate PIC on SCP promoter | |||||||||
![]() | TFIID-based intermediate PIC on SCP promoter | |||||||||
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機能・相同性 | ![]() spermine transport / negative regulation of MHC class I biosynthetic process / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / transcription factor TFTC complex ...spermine transport / negative regulation of MHC class I biosynthetic process / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / transcription factor TFTC complex / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / negative regulation of MHC class II biosynthetic process / transcription factor TFIIE complex / regulation of cell cycle G1/S phase transition / RNA polymerase transcription factor SL1 complex / RNA polymerase I general transcription initiation factor activity / phosphatase activator activity / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / transcription open complex formation at RNA polymerase II promoter / 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 / hepatocyte differentiation / 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 / transcription factor TFIIF complex / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of response to cytokine stimulus / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / positive regulation of androgen receptor activity / transcription factor TFIIA complex / female germ cell nucleus / C2H2 zinc finger domain binding / male pronucleus / female pronucleus / positive regulation by host of viral transcription / transcription regulator inhibitor activity / Abortive elongation of HIV-1 transcript in the absence of Tat / nuclear vitamin D receptor binding / RNA polymerase binding / germinal vesicle / RNA polymerase II general transcription initiation factor binding / limb development / box C/D snoRNP assembly / regulation of fat cell differentiation / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / SAGA complex / transcription preinitiation complex / RNA Polymerase I Transcription Termination / inner cell mass cell proliferation / Viral Messenger RNA Synthesis / response to L-glutamate / cellular response to ATP / Signaling by FGFR2 IIIa TM / midbrain development / histone acetyltransferase binding / 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 / RNA polymerase II general transcription initiation factor activity / mRNA Capping / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein acetylation / cell division site / HIV Transcription Initiation 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.7 Å | |||||||||
![]() | Chen X / Qi Y / Wang X / Wu Z / Li J / Xu Y | |||||||||
![]() | ![]() タイトル: Structural insights into preinitiation complex assembly on core promoters. 著者: Xizi Chen / Yilun Qi / Zihan Wu / Xinxin Wang / Jiabei Li / Dan Zhao / Haifeng Hou / Yan Li / Zishuo Yu / Weida Liu / Mo Wang / Yulei Ren / Ze Li / Huirong Yang / Yanhui Xu / ![]() 要旨: Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the ...Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the structures of human TFIID-based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA-TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)-activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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 | ![]() | 397.8 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 69.7 KB 69.7 KB | 表示 表示 | ![]() |
画像 | ![]() | 112.5 KB | ||
その他 | ![]() ![]() ![]() | 1.5 MB 9.4 MB 10.5 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7eg9MC ![]() 7edxC ![]() 7eg7C ![]() 7eg8C ![]() 7egaC ![]() 7egbC ![]() 7egcC ![]() 7egdC ![]() 7egeC ![]() 7egfC ![]() 7eggC ![]() 7eghC ![]() 7egiC ![]() 7egjC 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 ( |
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類似構造データ |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | TFIID-based intermediate PIC on SCP promoter | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 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
-追加マップ: 3.6 Angstrom TBP module
ファイル | emd_31109_additional_1.map | ||||||||||||
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注釈 | 3.6 Angstrom TBP module | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 2.9 Angstrom Pol II module
ファイル | emd_31109_additional_2.map | ||||||||||||
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注釈 | 2.9 Angstrom Pol II module | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 3.9 Angstrom TFIID module
ファイル | emd_31109_additional_3.map | ||||||||||||
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注釈 | 3.9 Angstrom TFIID module | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : TFIID-based intermediate PIC on SCP promoter
+超分子 #1: TFIID-based intermediate PIC on SCP promoter
+超分子 #2: TFIID
+超分子 #3: RNA POLYMERASE II
+超分子 #4: TFIIA
+超分子 #5: TFIIB
+超分子 #6: TFIIF
+超分子 #7: DNA(SCP promoters)
+超分子 #8: TFIIE
+分子 #1: Transcription initiation factor TFIID subunit 1
+分子 #2: Transcription initiation factor TFIID subunit 2
+分子 #3: Transcription initiation factor TFIID subunit 4
+分子 #4: Transcription initiation factor TFIID subunit 5
+分子 #5: Transcription initiation factor TFIID subunit 6
+分子 #6: Transcription initiation factor TFIID subunit 7
+分子 #7: Transcription initiation factor TFIID subunit 8
+分子 #8: Transcription initiation factor TFIID subunit 9
+分子 #9: Transcription initiation factor TFIID subunit 10
+分子 #10: Transcription initiation factor TFIID subunit 12
+分子 #11: Transcription initiation factor IIA subunit 2
+分子 #12: TATA-box-binding protein
+分子 #13: Transcription initiation factor IIA subunit 1
+分子 #14: Transcription initiation factor IIB
+分子 #15: General transcription factor IIF subunit 1
+分子 #16: General transcription factor IIF subunit 2
+分子 #17: General transcription factor IIE subunit 1
+分子 #18: Transcription initiation factor IIE subunit beta
+分子 #21: Transcription initiation factor TFIID subunit 3
+分子 #22: Transcription initiation factor TFIID subunit 11
+分子 #23: Transcription initiation factor TFIID subunit 13
+分子 #24: RPB1
+分子 #25: DNA-directed RNA polymerase subunit beta
+分子 #26: DNA-directed RNA polymerase II subunit RPB3
+分子 #27: DNA-directed RNA polymerase II subunit RPB4
+分子 #28: DNA-directed RNA polymerase II subunit E
+分子 #29: DNA-directed RNA polymerase II subunit F
+分子 #30: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #31: DNA-directed RNA polymerase II subunit RPB9
+分子 #32: RPB10
+分子 #33: RNA_pol_L_2 domain-containing protein
+分子 #34: RPB12
+分子 #35: DNA-directed RNA polymerase II subunit RPB7
+分子 #19: DNA (79-MER)
+分子 #20: DNA (79-MER)
+分子 #36: ZINC ION
+分子 #37: 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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.9 |
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凍結 | 凍結剤: ETHANE |
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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 K2 SUMMIT (4k 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: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 57889 |
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初期 角度割当 | タイプ: OTHER |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |