登録情報 データベース : EMDB / ID : EMD-12449 構造の表示 ダウンロードとリンクタイトル RNA polymerase II-Spt4/5-nucleosome-Chd1 structure マップデータMap D 詳細 試料複合体 : RNA polymerase II-Spt4/5-Chd1-nucleosomeタンパク質・ペプチド : x 19種DNA : x 2種RNA : x 1種リガンド : x 4種 詳細 キーワード chromatin remodelling / transcription / nucleosome / chromatin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
negative regulation of transcription elongation by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / snRNP binding / negative regulation of DNA-templated DNA replication / regulation of rRNA processing / RNA polymerase I core binding / regulation of chromatin organization ... negative regulation of transcription elongation by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / snRNP binding / negative regulation of DNA-templated DNA replication / regulation of rRNA processing / RNA polymerase I core binding / regulation of chromatin organization / DSIF complex / intracellular mRNA localization / rDNA binding / RNA polymerase I general transcription initiation factor binding / nucleosome organization / SLIK (SAGA-like) complex / regulation of transcription elongation by RNA polymerase II / RPB4-RPB7 complex / U4 snRNA binding / sister chromatid cohesion / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / ATP-dependent chromatin remodeler activity / SAGA complex / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / 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 / termination of RNA polymerase II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / termination of RNA polymerase I transcription / spliceosomal complex assembly / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / chromosome, centromeric region / Dual incision in TC-NER / transcription elongation by RNA polymerase I / U5 snRNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / ATP-dependent activity, acting on DNA / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / U2 snRNA binding / U6 snRNA binding / tRNA transcription by RNA polymerase III / positive regulation of autophagy / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / U1 snRNA binding / translation initiation factor binding / methylated histone binding / helicase activity / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / P-body / ribonucleoside binding / chromatin DNA binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / structural constituent of chromatin / peroxisome / nucleosome / nucleosome assembly / ribosome biogenesis / chromosome / single-stranded DNA binding / histone binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding 類似検索 - 分子機能 Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger ... Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5 C-terminal domain / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / Chromo domain, conserved site / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / : / NusG, N-terminal domain superfamily / Chromo/chromo shadow domain / Chromatin organization modifier domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal 類似検索 - ドメイン・相同性 Transcription elongation factor SPT4 / Histone H2B 1.1 / DNA-directed RNA polymerase II subunit RPB1 / Histone H2A type 1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ... Transcription elongation factor SPT4 / Histone H2B 1.1 / DNA-directed RNA polymerase II subunit RPB1 / Histone H2A type 1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB9 / Chromo domain-containing protein 1 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Histone H4 / Histone H3.2 類似検索 - 構成要素生物種 Saccharomyces cerevisiae (パン酵母) / Xenopus laevis (アフリカツメガエル) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) / synthetic construct (人工物) 手法 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度 : 2.9 Å 詳細 データ登録者Farnung L / Ochmann M / Engeholm M / Cramer P 資金援助 European Union, ドイツ, 4件 詳細 詳細を隠すOrganization Grant number 国 European Research Council (ERC) 693023 European Union German Research Foundation (DFG) SFB860 ドイツ German Research Foundation (DFG) SPP2191 ドイツ German Research Foundation (DFG) EXC 2067/1- 390729940 ドイツ
引用ジャーナル : Nat Struct Mol Biol / 年 : 2021タイトル : Structural basis of nucleosome transcription mediated by Chd1 and FACT.著者 : Lucas Farnung / Moritz Ochmann / Maik Engeholm / Patrick Cramer / 要旨 : Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is ... Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is facilitated by the chromatin remodeler Chd1 and the histone chaperone FACT when the elongation factors Spt4/5 and TFIIS are present. We report cryo-EM structures of transcribing Saccharomyces cerevisiae Pol II-Spt4/5-nucleosome complexes with bound Chd1 or FACT. In the first structure, Pol II transcription exposes the proximal histone H2A-H2B dimer that is bound by Spt5. Pol II has also released the inhibitory DNA-binding region of Chd1 that is poised to pump DNA toward Pol II. In the second structure, Pol II has generated a partially unraveled nucleosome that binds FACT, which excludes Chd1 and Spt5. These results suggest that Pol II progression through a nucleosome activates Chd1, enables FACT binding and eventually triggers transfer of FACT together with histones to upstream DNA. 履歴 登録 2021年2月19日 - ヘッダ(付随情報) 公開 2021年8月25日 - マップ公開 2021年8月25日 - 更新 2024年7月10日 - 現状 2024年7月10日 処理サイト : PDBe / 状態 : 公開
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