登録情報 データベース : EMDB / ID : EMD-16274 ダウンロードとリンクタイトル RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) マップデータ 詳細 試料複合体 : RNA polymerase II pre-initiation complex with the distal +1 nucleosome複合体 : General transcription factor IIH複合体 : Mammalian RNA polymerase II複合体 : Nucleosome (protein)複合体 : Nucleosome (DNA)複合体 : General transcription factor IIB複合体 : TATA-box binding protein複合体 : General transcription factor IIF複合体 : General transcription factor IIA複合体 : General transcription factor IIEタンパク質・ペプチド : x 2種 残り6件を表示 表示を減らすタンパク質・ペプチド : x 1種リガンド : x 3種 詳細 キーワード Mammalian PIC / +1 nucleosome / transcription initiation / TRANSCRIPTION機能・相同性 機能・相同性情報分子機能 ドメイン・相同性 構成要素
MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / central nervous system myelin formation / positive regulation of core promoter binding / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 kinase activity / RNA polymerase II CTD heptapeptide repeat T4 kinase activity / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / RNA polymerase II CTD heptapeptide repeat S7 kinase activity ... MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / central nervous system myelin formation / positive regulation of core promoter binding / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 kinase activity / RNA polymerase II CTD heptapeptide repeat T4 kinase activity / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / RNA polymerase II CTD heptapeptide repeat S7 kinase activity / RNA polymerase II core complex assembly / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / ventricular system development / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / RNA polymerase transcription factor SL1 complex / nucleotide-excision repair, preincision complex assembly / meiotic sister chromatid cohesion / phosphatase activator activity / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / RNA polymerase III general transcription initiation factor activity / TFIIF-class transcription factor complex binding / UV protection / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase I core promoter sequence-specific DNA binding / transcription factor TFIIF complex / embryonic cleavage / adult heart development / DNA 5'-3' helicase / 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 - 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 / mRNA Splicing - Major Pathway / 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 / transcription factor TFIIA complex / G protein-coupled receptor internalization / RNA Polymerase III Abortive And Retractive Initiation / female germ cell nucleus / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / male pronucleus / nuclear lumen / female pronucleus / germinal vesicle / RNA polymerase II general transcription initiation factor binding / [RNA-polymerase]-subunit kinase / nuclear thyroid hormone receptor binding / Abortive elongation of HIV-1 transcript in the absence of Tat / cyclin-dependent protein serine/threonine kinase regulator activity / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / transcription preinitiation complex / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / DNA 3'-5' helicase / Signaling by FGFR2 IIIa TM / protein acetylation / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 3'-5' DNA helicase activity / cell division site / spinal cord development / erythrocyte maturation / hematopoietic stem cell proliferation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / : / bone mineralization / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / 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 類似検索 - 分子機能 Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / CyclinH/Ccl1 / Cyclin-dependent kinase 7 / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like ... Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / CyclinH/Ccl1 / Cyclin-dependent kinase 7 / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Helical and beta-bridge domain / Helical and beta-bridge domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor TFIIE beta subunit, DNA-binding domain / TFIIH subunit TTDA/Tfb5 / Transcription initiation factor TFIIE, beta subunit / TFB5-like superfamily / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / Transcription factor TFIIH complex subunit Tfb5 / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription factor TFIIH complex subunit Tfb5 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / ATP-dependent helicase Rad3/Chl1-like / : / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Cyclin/Cyclin-like subunit Ssn8 / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) 類似検索 - ドメイン・相同性 DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC4 ... DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / Histone H2B 1.1 / Histone H2A type 1 / General transcription factor IIF subunit 2 / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase/translocase subunit XPB / TATA-box-binding protein / General transcription factor IIE subunit 1 / Transcription initiation factor IIE subunit beta / General transcription factor IIH subunit 1 / General transcription factor IIF subunit 1 / Cyclin-dependent kinase 7 / Cyclin-H / CDK-activating kinase assembly factor MAT1 / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB9 / Histone H4 / Histone H3.2 / Transcription initiation factor IIB / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4 類似検索 - 構成要素生物種 Homo sapiens (ヒト) / Sus scrofa (ブタ) / Xenopus laevis (アフリカツメガエル) / unidentified adenovirus (ウイルス)手法 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度 : 4.0 Å 詳細 データ登録者Abril-Garrido J / Dienemann C / Grabbe F / Velychko T / Lidschreiber M / Wang H / Cramer P 資金援助 ドイツ, European Union, 2件 詳細 詳細を隠すOrganization Grant number 国 German Research Foundation (DFG) ドイツ European Research Council (ERC) European Union
引用ジャーナル : Mol Cell / 年 : 2023タイトル : Structural basis of transcription reduction by a promoter-proximal +1 nucleosome.著者 : Julio Abril-Garrido / Christian Dienemann / Frauke Grabbe / Taras Velychko / Michael Lidschreiber / Haibo Wang / Patrick Cramer / 要旨 : At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further ... At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further upstream, at a promoter-proximal location. Here, we establish a model system to show that a promoter-proximal +1 nucleosome can reduce RNA synthesis in vivo and in vitro, and we analyze its structural basis. We find that the PIC assembles normally when the edge of the +1 nucleosome is located 18 base pairs (bp) downstream of the transcription start site (TSS). However, when the nucleosome edge is located further upstream, only 10 bp downstream of the TSS, the PIC adopts an inhibited state. The transcription factor IIH (TFIIH) shows a closed conformation and its subunit XPB contacts DNA with only one of its two ATPase lobes, inconsistent with DNA opening. These results provide a mechanism for nucleosome-dependent regulation of transcription initiation. 履歴 登録 2022年12月20日 - ヘッダ(付随情報) 公開 2023年5月3日 - マップ公開 2023年5月3日 - 更新 2024年7月24日 - 現状 2024年7月24日 処理サイト : PDBe / 状態 : 公開
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