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基本情報
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タイトル | Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. | |||||||||
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![]() | transcribing complex / de novo transcription initiation / initially transcribing complex (ITC) / TRANSCRIPTION | |||||||||
機能・相同性 | ![]() spermine transport / negative regulation of MHC class I biosynthetic process / P-TEFb complex binding / 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 ...spermine transport / negative regulation of MHC class I biosynthetic process / P-TEFb complex binding / 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 / hair cell differentiation / ventricular system development / nucleotide-excision repair factor 3 complex / transcription factor TFIIE 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 / SLIK (SAGA-like) complex / 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 / DNA 5'-3' helicase / hepatocyte differentiation / transcriptional start site selection at RNA polymerase II promoter / 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 / adult heart development / RNA Polymerase III Abortive And Retractive Initiation / positive regulation of androgen receptor activity / transcription factor TFIIA complex / female germ cell nucleus / G protein-coupled receptor internalization / 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 / nuclear vitamin D receptor binding / RNA polymerase binding / germinal vesicle / RNA polymerase II general transcription initiation factor binding / limb development / box C/D snoRNP assembly / regulation of fat cell differentiation 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.29 Å | |||||||||
![]() | 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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![]() | ![]() 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. | |||||||||
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マップデータ | ![]() | 12.8 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 95.5 KB 95.5 KB | 表示 表示 | ![]() |
画像 | ![]() | 74.5 KB | ||
Filedesc metadata | ![]() | 21.4 KB | ||
その他 | ![]() ![]() ![]() | 3 MB 112.2 MB 112.2 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 8waqMC ![]() 8wakC ![]() 8walC ![]() 8wanC ![]() 8waoC ![]() 8wapC ![]() 8warC ![]() 8wasC ![]() 8watC ![]() 8wauC ![]() 8wavC ![]() 8wawC ![]() 8waxC ![]() 8wayC ![]() 8wazC ![]() 8wb0C C: 同じ文献を引用 ( 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 | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.334 Å | ||||||||||||||||||||
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: Pol II module of TC7
ファイル | emd_37401_additional_1.map | ||||||||||||
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注釈 | Pol II module of TC7 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_37401_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_37401_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : Structure of transcribing complex 7 (TC7), the initially transcri...
+超分子 #1: Structure of transcribing complex 7 (TC7), the initially transcri...
+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
+超分子 #8: TFIIH
+超分子 #9: RNA
+超分子 #10: Alpha-amanitin
+超分子 #11: TFIIE
+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: Alpha-amanitin
+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 beta chain
+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 subunit
+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: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #44: DNA-directed RNA polymerase II subunit RPB11-a
+分子 #45: RPB12
+分子 #10: RNA
+分子 #29: non-template DNA
+分子 #30: template DNA
+分子 #46: ZINC ION
+分子 #47: IRON/SULFUR CLUSTER
+分子 #48: MAGNESIUM ION
+分子 #49: [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-pur...
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.9 |
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凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.5 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 6.29 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 5257 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |