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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-31111 | |||||||||
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タイトル | TFIID-based holo PIC on SCP promoter | |||||||||
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![]() | TFIID / preinitiation complex / core promoter / transcription initiation / TRANSCRIPTION | |||||||||
機能・相同性 | ![]() microfibril binding / spermine transport / negative regulation of MHC class I biosynthetic process / core TFIIH complex portion of holo TFIIH complex / MMXD complex / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex ...microfibril binding / spermine transport / negative regulation of MHC class I biosynthetic process / core TFIIH complex portion of holo TFIIH complex / MMXD complex / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / negative regulation of protein autoubiquitination / central nervous system myelin formation / DNA 5'-3' helicase / transcription factor TFTC complex / positive regulation of mitotic recombination / positive regulation of core promoter binding / meiotic sister chromatid cohesion / negative regulation of MHC class II biosynthetic process / hair follicle maturation / cyclin-dependent protein kinase activating kinase holoenzyme complex / hair cell differentiation / ventricular system development / TFIIH-class transcription factor complex binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / snRNA transcription by RNA polymerase II / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / SLIK (SAGA-like) complex / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIK complex / UV protection / 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 / 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 / RNA polymerase II core complex assembly / hepatocyte differentiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 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 / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / positive regulation of response to cytokine stimulus / positive regulation of androgen receptor activity / maintenance of protein location in nucleus / adult heart development / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / G protein-coupled receptor internalization / female germ cell nucleus / C2H2 zinc finger domain binding / male pronucleus / transcription factor TFIIH core complex / female pronucleus / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / transcription regulator inhibitor activity / DNA 3'-5' helicase / 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 / [RNA-polymerase]-subunit kinase 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: 3.3 Å | |||||||||
![]() | Chen X / Wu Z | |||||||||
資金援助 | 1件
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![]() | ![]() 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 | ![]() | 284.5 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 84.5 KB 84.5 KB | 表示 表示 | ![]() |
画像 | ![]() | 74 KB | ||
その他 | ![]() ![]() | 4.7 MB 1.9 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 390.7 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 390.2 KB | 表示 | |
XML形式データ | ![]() | 8 KB | 表示 | |
CIF形式データ | ![]() | 9.3 KB | 表示 | |
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 | ![]() 7egbMC ![]() 7edxC ![]() 7eg7C ![]() 7eg8C ![]() 7eg9C ![]() 7egaC ![]() 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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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: 2.8 Angstrom Pol II module
ファイル | emd_31111_additional_1.map | ||||||||||||
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注釈 | 2.8 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: 3.4 Angstrom TBP module
ファイル | emd_31111_additional_2.map | ||||||||||||
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注釈 | 3.4 Angstrom TBP 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 holo PIC on SCP promoter
+超分子 #1: TFIID-based holo 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: TFIIH
+分子 #1: CDK-activating kinase assembly factor MAT1
+分子 #2: General transcription factor IIH subunit 1
+分子 #3: General transcription factor IIH subunit 2
+分子 #4: General transcription factor IIH subunit 3
+分子 #5: General transcription factor IIH subunit 4
+分子 #6: General transcription factor IIH subunit 5
+分子 #7: General transcription and DNA repair factor IIH helicase subunit XPB
+分子 #8: General transcription and DNA repair factor IIH helicase subunit XPD
+分子 #9: Cyclin-dependent kinase 7
+分子 #10: Cyclin-H
+分子 #11: Transcription initiation factor TFIID subunit 1
+分子 #12: Transcription initiation factor TFIID subunit 2
+分子 #13: Transcription initiation factor TFIID subunit 4
+分子 #14: Transcription initiation factor TFIID subunit 5
+分子 #15: Transcription initiation factor TFIID subunit 6
+分子 #16: Transcription initiation factor TFIID subunit 7
+分子 #17: Transcription initiation factor TFIID subunit 8
+分子 #18: Transcription initiation factor TFIID subunit 9
+分子 #19: Transcription initiation factor TFIID subunit 10
+分子 #20: Transcription initiation factor TFIID subunit 12
+分子 #21: Transcription initiation factor IIA subunit 2
+分子 #22: TATA-box-binding protein
+分子 #23: Transcription initiation factor IIA subunit 1
+分子 #24: Transcription initiation factor IIB
+分子 #25: General transcription factor IIF subunit 1
+分子 #26: General transcription factor IIF subunit 2
+分子 #27: General transcription factor IIE subunit 1
+分子 #28: Transcription initiation factor IIE subunit beta
+分子 #31: Transcription initiation factor TFIID subunit 3
+分子 #32: Transcription initiation factor TFIID subunit 11
+分子 #33: Transcription initiation factor TFIID subunit 13
+分子 #34: DNA-directed RNA polymerase II subunit RPB1
+分子 #35: DNA-directed RNA polymerase subunit beta
+分子 #36: DNA-directed RNA polymerase II subunit RPB3
+分子 #37: DNA-directed RNA polymerase II subunit RPB4
+分子 #38: DNA-directed RNA polymerase II subunit E
+分子 #39: DNA-directed RNA polymerase II subunit F
+分子 #40: DNA-directed RNA polymerase II subunit RPB7
+分子 #41: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #42: DNA-directed RNA polymerase II subunit RPB9
+分子 #43: RPB10
+分子 #44: RNA_pol_L_2 domain-containing protein
+分子 #45: RPB12
+分子 #29: DNA (69-MER)
+分子 #30: DNA (69-MER)
+分子 #46: ZINC ION
+分子 #47: IRON/SULFUR CLUSTER
+分子 #48: 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 / 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): 1.5 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
初期モデル | モデルのタイプ: NONE |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 92806 |
初期 角度割当 | タイプ: OTHER |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |