+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8wap | ||||||
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タイトル | Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. | ||||||
要素 |
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キーワード | TRANSCRIPTION / transcribing complex / de novo transcription initiation / initially transcribing complex (ITC) | ||||||
機能・相同性 | 機能・相同性情報 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 / pre-snoRNP complex / Cytosolic iron-sulfur cluster assembly ...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 / pre-snoRNP complex / Cytosolic iron-sulfur cluster assembly / TFIIH-class transcription factor complex binding / nucleotide-excision repair, DNA duplex unwinding / negative regulation of protein autoubiquitination / central nervous system myelin formation / 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 / negative regulation of MHC class II biosynthetic process / hair follicle maturation / ventricular system development / hair cell differentiation / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / SLIK (SAGA-like) complex / regulation of cell cycle G1/S phase transition / RNA polymerase transcription factor SL1 complex / RNA polymerase I general transcription initiation factor activity / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIK complex / UV protection / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / 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 I core promoter sequence-specific DNA binding / hepatocyte differentiation / transcriptional start site selection at RNA polymerase II promoter / DNA 5'-3' helicase / 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 / 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 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription factor TFIIF complex / positive regulation of response to cytokine stimulus / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / G protein-coupled receptor internalization / adult heart development / positive regulation of androgen receptor activity / transcription factor TFIIA complex / female germ cell nucleus / C2H2 zinc finger domain binding / male pronucleus / transcription factor TFIIH core complex / female pronucleus / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / transcription regulator inhibitor activity / Abortive elongation of HIV-1 transcript in the absence of Tat / DNA 3'-5' helicase / RNA polymerase II general transcription initiation factor binding / germinal vesicle / nuclear vitamin D receptor binding / RNA polymerase binding / SAGA complex / limb development / transcription preinitiation complex / regulation of fat cell differentiation 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Amanita phalloides (タマゴテングタケ) Sus scrofa (ブタ) synthetic construct (人工物) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 5.85 Å | ||||||
データ登録者 | Chen, X. / Liu, W. / Wang, Q. / Wang, X. / Ren, Y. / Qu, X. / Li, W. / Xu, Y. | ||||||
資金援助 | 1件
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引用 | ジャーナル: Science / 年: 2023 タイトル: Structural visualization of transcription initiation in action. 著者: Xizi Chen / Weida Liu / Qianmin Wang / Xinxin Wang / Yulei Ren / Xuechun Qu / Wanjun Li / Yanhui Xu / 要旨: Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted ...Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted on G-less promoters when nascent RNAs reach 2 to 17 nucleotides in length, respectively. Connecting these structures generated a movie and a working model. As initially synthesized RNA grows, general transcription factors (GTFs) remain bound to the promoter and the transcription bubble expands. Nucleoside triphosphate (NTP)-driven RNA-DNA translocation and template-strand accumulation in a nearly sealed channel may promote the transition from initially transcribing complexes (ITCs) (TC2 to TC9) to early elongation complexes (EECs) (TC10 to TC17). Our study shows dynamic processes of transcription initiation and reveals why ITCs require GTFs and bubble expansion for initial RNA synthesis, whereas EECs need GTF dissociation from the promoter and bubble collapse for promoter escape. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8wap.cif.gz | 2.5 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8wap.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 8wap.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8wap_validation.pdf.gz | 1.8 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8wap_full_validation.pdf.gz | 1.8 MB | 表示 | |
XML形式データ | 8wap_validation.xml.gz | 281.1 KB | 表示 | |
CIF形式データ | 8wap_validation.cif.gz | 477.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/wa/8wap ftp://data.pdbj.org/pub/pdb/validation_reports/wa/8wap | HTTPS FTP |
-関連構造データ
関連構造データ | 37400MC 8wakC 8walC 8wanC 8waoC 8waqC 8warC 8wasC 8watC 8wauC 8wavC 8wawC 8waxC 8wayC 8wazC 8wb0C M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
+タンパク質 , 4種, 4分子 0PUz
+General transcription factor IIH subunit ... , 5種, 5分子 12345
+General transcription and DNA repair factor IIH helicase subunit ... , 2種, 2分子 67
+Transcription initiation factor ... , 17種, 23分子 ABDdEeFfGHIiJjLlOQRVckm
+General transcription factor IIF subunit ... , 2種, 2分子 ST
+DNA鎖 , 2種, 2分子 XY
+DNA-directed RNA polymerase ... , 9種, 9分子 opqrstuwy
+DNA-directed RNA polymerases I, II, and III subunit ... , 2種, 2分子 vx
+タンパク質・ペプチド / RNA鎖 , 2種, 2分子 NZ
+非ポリマー , 4種, 20分子
+詳細
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 |
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由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 1500 nm |
撮影 | 電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
CTF補正 | タイプ: NONE |
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3次元再構成 | 解像度: 5.85 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 4867 / 対称性のタイプ: POINT |