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- EMDB-34359: PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state -
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データを開く
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基本情報
登録情報 | ![]() | |||||||||
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タイトル | PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state | |||||||||
![]() | PIC-Mediator in complex with plus 1 nucleosome (T40N) in MH-binding state | |||||||||
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機能・相同性 | ![]() positive regulation of mediator complex assembly / positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / spermine transport / negative regulation of MHC class I biosynthetic process / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / core TFIIH complex portion of holo TFIIH complex / MMXD complex ...positive regulation of mediator complex assembly / positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / spermine transport / negative regulation of MHC class I biosynthetic process / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / core TFIIH complex portion of holo TFIIH complex / MMXD complex / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / SAGA complex assembly / lateral mesodermal cell differentiation / mammary gland branching involved in thelarche / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / G0 to G1 transition / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / thyroid hormone receptor signaling pathway / negative regulation of protein autoubiquitination / central nervous system myelin formation / DNA 5'-3' helicase / transcription factor TFTC complex / positive regulation of mitotic recombination / positive regulation of core promoter binding / core mediator complex / regulation of vitamin D receptor signaling pathway / meiotic sister chromatid cohesion / negative regulation of MHC class II biosynthetic process / hair follicle maturation / cyclin-dependent protein kinase activating kinase holoenzyme complex / hair cell differentiation / ventricular system development / TFIIH-class transcription factor complex binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / snRNA transcription by RNA polymerase II / 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 / 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 / RNA polymerase transcription factor SL1 complex / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / 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 / RNA polymerase II core complex assembly / hepatocyte differentiation / ventricular trabecula myocardium morphogenesis / 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 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / thyroid hormone generation / nuclear retinoic acid receptor binding / positive regulation of response to cytokine stimulus / positive regulation of androgen receptor activity / mediator complex / maintenance of protein location in nucleus / positive regulation of keratinocyte differentiation / adult heart development / Generic Transcription Pathway 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: 5.04 Å | |||||||||
![]() | Chen X / Wang X / Liu W / Ren Y / Qu X / Li J / Yin X / Xu Y | |||||||||
資金援助 | 1件
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![]() | ![]() タイトル: Structures of +1 nucleosome-bound PIC-Mediator complex. 著者: Xizi Chen / Xinxin Wang / Weida Liu / Yulei Ren / Xuechun Qu / Jiabei Li / Xiaotong Yin / Yanhui Xu / ![]() 要旨: RNA polymerase II-mediated eukaryotic transcription starts with the assembly of the preinitiation complex (PIC) on core promoters. The +1 nucleosome is well positioned about 40 base pairs downstream ...RNA polymerase II-mediated eukaryotic transcription starts with the assembly of the preinitiation complex (PIC) on core promoters. The +1 nucleosome is well positioned about 40 base pairs downstream of the transcription start site (TSS) and is commonly known as a barrier of transcription. The +1 nucleosome-bound PIC-Mediator structures show that PIC-Mediator prefers binding to T40N nucleosome located 40 base pairs downstream of TSS and contacts T50N but not the T70N nucleosome. The nucleosome facilitates the organization of PIC-Mediator on the promoter by binding TFIIH subunit p52 and Mediator subunits MED19 and MED26 and may contribute to transcription initiation. PIC-Mediator exhibits multiple nucleosome-binding patterns, supporting a structural role of the +1 nucleosome in the coordination of PIC-Mediator assembly. Our study reveals the molecular mechanism of PIC-Mediator organization on chromatin and underscores the significance of the +1 nucleosome in regulating transcription initiation. | |||||||||
履歴 |
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構造の表示
添付画像 |
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-EMDBアーカイブ
マップデータ | ![]() | 18.6 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 145.3 KB 145.3 KB | 表示 表示 | ![]() |
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その他 | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 34.5 MB 25.2 MB 8.6 MB 111.1 MB 23.2 MB 113.3 MB 52.9 MB 52.4 MB 113.3 MB 49.1 MB 261.2 MB 261.2 MB | ||
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-検証レポート
文書・要旨 | ![]() | 716.7 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 716.3 KB | 表示 | |
XML形式データ | ![]() | 16.5 KB | 表示 | |
CIF形式データ | ![]() | 19.6 KB | 表示 | |
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-関連構造データ
関連構造データ | ![]() 8gxqMC ![]() 8gxsC 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
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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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注釈 | PIC-Mediator in complex with plus 1 nucleosome (T40N) in MH-binding state | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.334 Å | ||||||||||||||||||||
密度 |
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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: PIC core of the T40N-bound PIC-Mediator
+追加マップ: Mediator middle module and TFIIH CAK module of...
+追加マップ: Nucleosome of the PIC-Mediator in complex with plus...
+追加マップ: Mediator of the T40N-bound PIC-Mediator
+追加マップ: Nucleosome of the T40N-bound PIC-Mediator
+追加マップ: Mediator tail module of the T40N-bound PIC-Mediator
+追加マップ: TFIIH of the T40N-bound PIC-Mediator
+追加マップ: TFIID of the T40N-bound PIC-Mediator
+追加マップ: Mediator head module of the T40N-bound PIC-Mediator
+追加マップ: Mediator middle module of the T40N-bound
+ハーフマップ: #2
+ハーフマップ: #1
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試料の構成要素
+全体 : PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state
+超分子 #1: PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state
+分子 #1: DNA (228-mer)
+分子 #2: DNA (228-mer)
+分子 #76: DNA (162-mer)
+分子 #77: DNA (162-mer)
+分子 #3: Transcription initiation factor IIB
+分子 #4: Transcription initiation factor TFIID subunit 1
+分子 #5: General transcription factor IIE subunit 1
+分子 #6: General transcription factor IIF subunit 1
+分子 #7: General transcription and DNA repair factor IIH helicase subunit XPD
+分子 #8: Histone H3
+分子 #9: DNA-directed RNA polymerase subunit
+分子 #10: Transcription initiation factor TFIID subunit 2
+分子 #11: Transcription initiation factor IIE subunit beta
+分子 #12: General transcription factor IIF subunit 2
+分子 #13: General transcription factor IIH subunit 1
+分子 #14: Histone H4
+分子 #15: DNA-directed RNA polymerase subunit beta
+分子 #16: General transcription factor IIH subunit 4
+分子 #17: DNA-directed RNA polymerase II subunit RPB3
+分子 #18: DNA-directed RNA polymerase II subunit E
+分子 #19: DNA-directed RNA polymerase II subunit F
+分子 #20: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #21: DNA-directed RNA polymerase II subunit RPB9
+分子 #22: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #23: RNA_pol_L_2 domain-containing protein
+分子 #24: RPB12
+分子 #25: TATA-box-binding protein
+分子 #26: Transcription initiation factor IIA subunit 1
+分子 #27: Transcription initiation factor IIA subunit 2
+分子 #28: Transcription initiation factor TFIID subunit 3
+分子 #29: Transcription initiation factor TFIID subunit 4
+分子 #30: Transcription initiation factor TFIID subunit 5
+分子 #31: Transcription initiation factor TFIID subunit 6
+分子 #32: Transcription initiation factor TFIID subunit 9
+分子 #33: Transcription initiation factor TFIID subunit 10
+分子 #34: Transcription initiation factor TFIID subunit 11
+分子 #35: Transcription initiation factor TFIID subunit 12
+分子 #36: Transcription initiation factor TFIID subunit 13
+分子 #37: Transcription initiation factor TFIID subunit 7
+分子 #38: Transcription initiation factor TFIID subunit 8
+分子 #39: CDK-activating kinase assembly factor MAT1
+分子 #40: General transcription factor IIH subunit 3
+分子 #41: General transcription factor IIH subunit 2
+分子 #42: General transcription and DNA repair factor IIH helicase subunit XPB
+分子 #43: General transcription factor IIH subunit 5
+分子 #44: Cyclin-dependent kinase 7
+分子 #45: Cyclin-H
+分子 #46: DNA-directed RNA polymerase II subunit RPB4
+分子 #47: DNA-directed RNA polymerase II subunit RPB7
+分子 #48: Mediator of RNA polymerase II transcription subunit 7
+分子 #49: Mediator of RNA polymerase II transcription subunit 10
+分子 #50: Mediator of RNA polymerase II transcription subunit 14
+分子 #51: Mediator of RNA polymerase II transcription subunit 19
+分子 #52: Mediator of RNA polymerase II transcription subunit 21
+分子 #53: Mediator of RNA polymerase II transcription subunit 1
+分子 #54: Mediator of RNA polymerase II transcription subunit 4
+分子 #55: Mediator of RNA polymerase II transcription subunit 6
+分子 #56: Mediator of RNA polymerase II transcription subunit 9
+分子 #57: Mediator of RNA polymerase II transcription subunit 31
+分子 #58: Mediator of RNA polymerase II transcription subunit 17
+分子 #59: Mediator of RNA polymerase II transcription subunit 26
+分子 #60: Mediator of RNA polymerase II transcription subunit 29
+分子 #61: Mediator of RNA polymerase II transcription subunit 27
+分子 #62: Mediator of RNA polymerase II transcription subunit 28
+分子 #63: Mediator of RNA polymerase II transcription subunit 30
+分子 #64: Mediator of RNA polymerase II transcription subunit 15
+分子 #65: Isoform 2 of Mediator of RNA polymerase II transcription subunit 8
+分子 #66: Mediator of RNA polymerase II transcription subunit 11
+分子 #67: Mediator of RNA polymerase II transcription subunit 18
+分子 #68: Mediator of RNA polymerase II transcription subunit 20
+分子 #69: Mediator of RNA polymerase II transcription subunit 22
+分子 #70: Isoform 2 of Mediator of RNA polymerase II transcription subunit 16
+分子 #71: Mediator of RNA polymerase II transcription subunit 23
+分子 #72: Mediator of RNA polymerase II transcription subunit 24
+分子 #73: Mediator of RNA polymerase II transcription subunit 25
+分子 #74: HISTONE H2A.Z
+分子 #75: Histone H2B
+分子 #78: ZINC ION
+分子 #79: IRON/SULFUR CLUSTER
+分子 #80: 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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![]() | 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
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 5.04 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 26458 |
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初期 角度割当 | タイプ: OTHER |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |