+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-31112 | |||||||||
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タイトル | p53-bound TFIID-based holo PIC on HDM2 promoter | |||||||||
マップデータ | p53-bound TFIID-based holo PIC on HDM2 promoter | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 microfibril binding / spermine transport / negative regulation of MHC class I biosynthetic process / MMXD complex / core TFIIH complex portion of holo TFIIH complex / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / TFIIH-class transcription factor complex binding ...microfibril binding / spermine transport / negative regulation of MHC class I biosynthetic process / MMXD complex / core TFIIH complex portion of holo TFIIH complex / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / TFIIH-class transcription factor complex binding / pre-snoRNP complex / positive regulation of DNA helicase activity / negative regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / negative regulation of protein autoubiquitination / transcription factor TFTC complex / positive regulation of mitotic recombination / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / hair cell differentiation / negative regulation of MHC class II biosynthetic process / ventricular system development / hair follicle maturation / cyclin-dependent protein kinase activating kinase holoenzyme complex / RNA polymerase transcription factor SL1 complex / snRNA transcription by RNA polymerase II / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / 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 / 紫外線 / CAK-ERCC2 complex / transcription factor TFIIK complex / nuclear DNA-directed RNA polymerase complex / RNA polymerase III general transcription initiation factor activity / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / positive regulation of response to cytokine stimulus / hepatocyte differentiation / maintenance of protein location in nucleus / 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 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 / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / 5'-3' DNA helicase activity / positive regulation of androgen receptor activity / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / box C/D snoRNP assembly / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / male pronucleus / transcription regulator inhibitor activity / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / SAGA complex / nuclear vitamin D receptor binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Sus scrofa (ブタ) / Human (ヒト) / Pig (ブタ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
データ登録者 | Chen X / Wu Z / Hou H / Qi Y / Wang X / Li J / 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_31112.map.gz | 285 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-31112-v30.xml emd-31112.xml | 90.9 KB 90.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_31112.png | 47.8 KB | ||
その他 | emd_31112_additional_1.map.gz emd_31112_additional_2.map.gz emd_31112_additional_3.map.gz emd_31112_additional_4.map.gz emd_31112_additional_5.map.gz emd_31112_additional_6.map.gz | 4.8 MB 262.9 MB 262 MB 15.5 MB 5.4 MB 21.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-31112 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31112 | HTTPS FTP |
-関連構造データ
関連構造データ | 7egcMC 7edxC 7eg7C 7eg8C 7eg9C 7egaC 7egbC 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 (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_31112.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | p53-bound TFIID-based holo PIC on HDM2 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: 2.9 Angstrom Pol II module
ファイル | emd_31112_additional_1.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: 3.5 Angstrom TBP module
ファイル | emd_31112_additional_2.map | ||||||||||||
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注釈 | 3.5 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: 3.5 Angstrom CAK module
ファイル | emd_31112_additional_3.map | ||||||||||||
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注釈 | 3.5 Angstrom CAK module | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 4.7 Angstrom TFIIH module
ファイル | emd_31112_additional_4.map | ||||||||||||
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注釈 | 4.7 Angstrom TFIIH module | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 4.5 Angstrom TFIID module
ファイル | emd_31112_additional_5.map | ||||||||||||
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注釈 | 4.5 Angstrom TFIID module | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 4.3 Angstrom TFIIE module
ファイル | emd_31112_additional_6.map | ||||||||||||
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注釈 | 4.3 Angstrom TFIIE module | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : p53-bound TFIID-based holo PIC on HDM2 promoter
+超分子 #1: p53-bound TFIID-based holo PIC on HDM2 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(HDM2 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 (71-MER)
+分子 #30: DNA (71-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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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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凍結 | 凍結剤: ETHANE |
-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 |
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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期 角度割当 | タイプ: OTHER |
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最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 42939 |