+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-31113 | |||||||||
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タイトル | SCP promoter-bound TFIID-TFIIA in initial TBP-loading state | |||||||||
マップデータ | SCP promoter-bound TFIID-TFIIA in initial TBP-loading state | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 spermine transport / negative regulation of MHC class I biosynthetic process / P-TEFb complex binding / 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 ...spermine transport / negative regulation of MHC class I biosynthetic process / P-TEFb complex binding / 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 / negative regulation of MHC class II biosynthetic process / regulation of cell cycle G1/S phase transition / RNA polymerase transcription factor SL1 complex / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / hepatocyte differentiation / 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 / 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 / nuclear vitamin D receptor binding / RNA polymerase binding / RNA polymerase II general transcription initiation factor binding / limb development / box C/D snoRNP assembly / regulation of fat cell differentiation / nuclear thyroid hormone receptor binding / SAGA complex / transcription preinitiation complex / RNA Polymerase I Transcription Termination / inner cell mass cell proliferation / response to L-glutamate / embryonic placenta development / cellular response to ATP / midbrain development / histone acetyltransferase binding / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 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 I Transcription Initiation / regulation of RNA splicing / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / aryl hydrocarbon receptor binding / transcription by RNA polymerase III / TFIIB-class transcription factor binding / RNA polymerase II transcribes snRNA genes / MLL1 complex / negative regulation of cell cycle / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / estrogen receptor signaling pathway / male germ cell nucleus / negative regulation of ubiquitin-dependent protein catabolic process / somitogenesis / regulation of DNA repair / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / RNA polymerase II preinitiation complex assembly / histone acetyltransferase activity / histone acetyltransferase / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / lysine-acetylated histone binding / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / response to interleukin-1 / SIRT1 negatively regulates rRNA expression / regulation of signal transduction by p53 class mediator / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / RNA Polymerase I Promoter Escape / nuclear receptor binding / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression 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: 6.75 Å | |||||||||
データ登録者 | Chen X / Wu Z / Li J / Zhao D / Xu Y | |||||||||
引用 | ジャーナル: Science / 年: 2021 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 |
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_31113.map.gz | 9.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-31113-v30.xml emd-31113.xml | 35.3 KB 35.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_31113.png | 96.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-31113 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31113 | HTTPS FTP |
-関連構造データ
関連構造データ | 7egdMC 7edxC 7eg7C 7eg8C 7eg9C 7egaC 7egbC 7egcC 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 (文献) |
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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_31113.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | SCP promoter-bound TFIID-TFIIA in initial TBP-loading state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.35 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 : SCP promoter-bound TFIID-TFIIA in initial TBP-loading state
+超分子 #1: SCP promoter-bound TFIID-TFIIA in initial TBP-loading state
+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 #16: Transcription initiation factor TFIID subunit 3
+分子 #17: Transcription initiation factor TFIID subunit 11
+分子 #18: Transcription initiation factor TFIID subunit 13
+分子 #14: DNA (72-MER)
+分子 #15: DNA (72-MER)
-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: 7.9 |
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK IV |
-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) 検出モード: SUPER-RESOLUTION / 平均電子線量: 50.0 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 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 6.75 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 100170 |
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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 |