+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9302 | |||||||||
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タイトル | Human TFIID Lobe A canonical | |||||||||
マップデータ | primary map | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / pre-snoRNP complex / negative regulation of protein autoubiquitination / transcription factor TFTC complex / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity ...SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / pre-snoRNP complex / negative regulation of protein autoubiquitination / transcription factor TFTC complex / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase transcription factor SL1 complex / 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 / positive regulation of androgen receptor activity / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / 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 / box C/D snoRNP assembly / RNA polymerase II general transcription initiation factor binding / SAGA complex / limb development / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / response to L-glutamate / cellular response to ATP / midbrain development / 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 / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / aryl hydrocarbon receptor binding / regulation of RNA splicing / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / MLL1 complex / transcription factor TFIID complex / TFIIB-class transcription factor binding / negative regulation of cell cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA polymerase II general transcription initiation factor activity / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / somitogenesis / positive regulation of intrinsic apoptotic signaling pathway / core promoter sequence-specific DNA binding / ovarian follicle development / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / negative regulation of ubiquitin-dependent protein catabolic process / response to interleukin-1 / SIRT1 negatively regulates rRNA expression / regulation of signal transduction by p53 class mediator / male germ cell nucleus / DNA-templated transcription initiation / promoter-specific chromatin binding / nuclear receptor binding / nuclear estrogen receptor binding / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / euchromatin / lysine-acetylated histone binding / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / multicellular organism growth / negative regulation of DNA-binding transcription factor activity / G1/S transition of mitotic cell cycle / protein polyubiquitination / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / actin cytoskeleton / positive regulation of protein binding / kinase activity 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: 9.8 Å | |||||||||
データ登録者 | Patel AB / Louder RK / Greber BJ / Grunberg S / Luo J / Fang J / Liu Y / Ranish J / Hahn S / Nogales E | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Science / 年: 2018 タイトル: Structure of human TFIID and mechanism of TBP loading onto promoter DNA. 著者: Avinash B Patel / Robert K Louder / Basil J Greber / Sebastian Grünberg / Jie Luo / Jie Fang / Yutong Liu / Jeff Ranish / Steve Hahn / Eva Nogales / 要旨: The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and ...The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and initiating PIC assembly. We used cryo-electron microscopy, chemical cross-linking mass spectrometry, and biochemical reconstitution to determine the complete molecular architecture of TFIID and define the conformational landscape of TFIID in the process of TATA box-binding protein (TBP) loading onto promoter DNA. Our structural analysis revealed five structural states of TFIID in the presence of TFIIA and promoter DNA, showing that the initial binding of TFIID to the downstream promoter positions the upstream DNA and facilitates scanning of TBP for a TATA box and the subsequent engagement of the promoter. Our findings provide a mechanistic model for the specific loading of TBP by TFIID onto the promoter. | |||||||||
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_9302.map.gz | 80.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9302-v30.xml emd-9302.xml | 28.7 KB 28.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9302.png | 37.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9302 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9302 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_9302_validation.pdf.gz | 360.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_9302_full_validation.pdf.gz | 359.9 KB | 表示 | |
XML形式データ | emd_9302_validation.xml.gz | 6.2 KB | 表示 | |
CIF形式データ | emd_9302_validation.cif.gz | 7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9302 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9302 | HTTPS FTP |
-関連構造データ
関連構造データ | 6mzdMC 9298C 9299C 9300C 9301C 9305C 9306C 6mzcC 6mzlC 6mzmC 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_9302.map.gz / 形式: CCP4 / 大きさ: 91.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.32 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 : General transcription factor IID
+超分子 #1: General transcription factor IID
+分子 #1: Transcription initiation factor TFIID subunit 1
+分子 #2: Transcription initiation factor TFIID subunit 3
+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 9
+分子 #7: Transcription initiation factor TFIID subunit 10
+分子 #8: Transcription initiation factor TFIID subunit 11
+分子 #9: Transcription initiation factor TFIID subunit 12
+分子 #10: Transcription initiation factor TFIID subunit 13
+分子 #11: TATA-box-binding protein
+分子 #12: poly(UNK)
-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 | .2 mg/mL | ||||||||||||||||
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緩衝液 | pH: 7.9 構成要素:
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凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV / 詳細: BT 4s; BF 15N. |
-電子顕微鏡法
顕微鏡 | FEI TITAN |
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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: 40.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm |
試料ステージ | 試料ホルダーモデル: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER ホルダー冷却材: NITROGEN |
-画像解析
CTF補正 | ソフトウェア - 名称: Gctf |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 9.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 107900 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION |