+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-31204 | |||||||||
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タイトル | TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) | |||||||||
マップデータ | TFIID-based PIC-MED holo-complex (deletion of MED1-IDR) in pre-assembled state (pre-hPIC-MED) | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 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 / MMXD complex / core TFIIH complex portion of holo TFIIH complex / SAGA 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 / MMXD complex / core TFIIH complex portion of holo TFIIH complex / SAGA complex assembly / lateral mesodermal cell differentiation / androgen biosynthetic process / positive regulation of G0 to G1 transition / DNA-templated transcription open complex formation / allantois development / mammary gland branching involved in thelarche / retinal pigment epithelium development / pre-snoRNP complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / TFIIH-class transcription factor complex binding / G0 to G1 transition / thyroid hormone receptor signaling pathway / negative regulation of protein autoubiquitination / central nervous system myelin formation / positive regulation of core promoter binding / transcription factor TFTC complex / RNA polymerase II core complex assembly / core mediator complex / positive regulation of mitotic recombination / meiotic sister chromatid cohesion / negative regulation of MHC class II biosynthetic process / hair follicle maturation / RNA polymerase transcription factor SL1 complex / ventricular system development / snRNA transcription by RNA polymerase II / hair cell differentiation / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / regulation of vitamin D receptor signaling pathway / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / phosphatase activator activity / nucleotide-excision repair, preincision complex assembly / SLIK (SAGA-like) complex / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / UV protection / transcription factor TFIIK complex / embryonic cleavage / transcription open complex formation 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 / TFIIF-class transcription factor complex binding / hepatocyte differentiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcriptional start site selection at RNA polymerase II 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 - 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 / ventricular trabecula myocardium morphogenesis / positive regulation of response to cytokine stimulus / thyroid hormone generation / transcription factor TFIIF complex / DNA 5'-3' helicase / mediator complex / nuclear retinoic acid receptor binding / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / adult heart development / positive regulation of androgen receptor activity / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / transcription factor TFIIA complex 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Sus scrofa (ブタ) / Pig (ブタ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.07 Å | |||||||||
データ登録者 | Chen X / Qi Y / Wang X / Wu Z / Yin X / Li J / Liu W / Xu Y | |||||||||
引用 | ジャーナル: Science / 年: 2021 タイトル: Structures of the human Mediator and Mediator-bound preinitiation complex. 著者: Xizi Chen / Xiaotong Yin / Jiabei Li / Zihan Wu / Yilun Qi / Xinxin Wang / Weida Liu / Yanhui Xu / 要旨: The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26- ...The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)-mediated phosphorylation of the Pol II C-terminal domain (CTD). We determined the structures of human Mediator in the Tail module-extended (at near-atomic resolution) and Tail-bent conformations and structures of TFIID-based PIC-Mediator (76 polypeptides, ~4.1 megadaltons) in four distinct conformations. PIC-Mediator assembly induces concerted reorganization (Head-tilting and Middle-down) of Mediator and creates a Head-Middle sandwich, which stabilizes two CTD segments and brings CTD to CDK7 for phosphorylation; this suggests a CTD-gating mechanism favorable for phosphorylation. The TFIID-based PIC architecture modulates Mediator organization and TFIIH stabilization, underscoring the importance of TFIID in orchestrating PIC-Mediator assembly. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_31204.map.gz | 277 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-31204-v30.xml emd-31204.xml | 133 KB 133 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_31204.png | 85.4 KB | ||
その他 | emd_31204_additional_1.map.gz emd_31204_additional_2.map.gz emd_31204_additional_3.map.gz emd_31204_additional_4.map.gz emd_31204_additional_5.map.gz emd_31204_additional_6.map.gz emd_31204_additional_7.map.gz | 3.7 MB 2.7 MB 3.8 MB 277.8 MB 11.8 MB 397.9 MB 2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-31204 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31204 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_31204_validation.pdf.gz | 341 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_31204_full_validation.pdf.gz | 340.5 KB | 表示 | |
XML形式データ | emd_31204_validation.xml.gz | 8.1 KB | 表示 | |
CIF形式データ | emd_31204_validation.cif.gz | 9.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31204 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31204 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_31204.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | TFIID-based PIC-MED holo-complex (deletion of MED1-IDR) in pre-assembled state (pre-hPIC-MED) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.3175 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-追加マップ: 7.1 Angstrom TFIID
ファイル | emd_31204_additional_1.map | ||||||||||||
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注釈 | 7.1 Angstrom TFIID | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 7.3 Angstrom TFIIH
ファイル | emd_31204_additional_2.map | ||||||||||||
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注釈 | 7.3 Angstrom TFIIH | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 4.0 Angstrom MED
ファイル | emd_31204_additional_3.map | ||||||||||||
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注釈 | 4.0 Angstrom MED | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 3.9 Angstrom MED-Head
ファイル | emd_31204_additional_4.map | ||||||||||||
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注釈 | 3.9 Angstrom MED-Head | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 6.2 Angstrom MED-Middle
ファイル | emd_31204_additional_5.map | ||||||||||||
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注釈 | 6.2 Angstrom MED-Middle | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 5.7 Angstrom CAK
ファイル | emd_31204_additional_6.map | ||||||||||||
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注釈 | 5.7 Angstrom CAK | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 3.7 Angstrom TBP
ファイル | emd_31204_additional_7.map | ||||||||||||
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注釈 | 3.7 Angstrom TBP | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre...
+超分子 #1: TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre...
+超分子 #2: TFIID
+超分子 #3: DNA-directed RNA polymerase
+超分子 #4: DNA
+超分子 #5: TFIIH
+超分子 #6: TFIIA
+超分子 #7: TFIIB
+超分子 #8: TFIIF
+超分子 #9: TFIIE
+超分子 #10: Mediator
+分子 #1: CDK-activating kinase assembly factor MAT1
+分子 #2: Cyclin-dependent kinase 7
+分子 #3: Cyclin-H
+分子 #4: Transcription initiation factor IIA subunit 2
+分子 #5: TATA-box-binding protein
+分子 #6: TFIIA-a
+分子 #7: Transcription initiation factor IIB
+分子 #8: General transcription factor IIF subunit 1
+分子 #9: General transcription factor IIF subunit 2
+分子 #10: RPB1
+分子 #11: DNA-directed RNA polymerase subunit beta
+分子 #12: DNA-directed RNA polymerase II subunit RPB3
+分子 #13: DNA-directed RNA polymerase II subunit RPB4
+分子 #14: DNA-directed RNA polymerase II subunit E
+分子 #15: DNA-directed RNA polymerase II subunit F
+分子 #16: DNA-directed RNA polymerase II subunit RPB7
+分子 #17: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #18: DNA-directed RNA polymerase II subunit RPB9
+分子 #19: RPB10
+分子 #20: RNA_pol_L_2 domain-containing protein
+分子 #21: RPB12
+分子 #22: Transcription initiation factor TFIID subunit 1
+分子 #23: Transcription initiation factor TFIID subunit 2
+分子 #24: Transcription initiation factor TFIID subunit 4
+分子 #25: Transcription initiation factor TFIID subunit 5
+分子 #26: Transcription initiation factor TFIID subunit 6
+分子 #27: Transcription initiation factor TFIID subunit 7
+分子 #28: Transcription initiation factor TFIID subunit 8
+分子 #29: Transcription initiation factor TFIID subunit 9
+分子 #30: Transcription initiation factor TFIID subunit 10
+分子 #31: Transcription initiation factor TFIID subunit 12
+分子 #32: Transcription initiation factor TFIID subunit 3
+分子 #33: Transcription initiation factor TFIID subunit 11
+分子 #34: Transcription initiation factor TFIID subunit 13
+分子 #35: General transcription factor IIE subunit 1
+分子 #36: Transcription initiation factor IIE subunit beta
+分子 #37: General transcription factor IIH subunit 1
+分子 #38: General transcription factor IIH subunit 2
+分子 #39: General transcription factor IIH subunit 3
+分子 #40: General transcription factor IIH subunit 4
+分子 #41: General transcription factor IIH subunit 5
+分子 #42: General transcription and DNA repair factor IIH helicase subunit XPB
+分子 #43: General transcription and DNA repair factor IIH helicase subunit XPD
+分子 #44: Mediator of RNA polymerase II transcription subunit 27
+分子 #45: Mediator of RNA polymerase II transcription subunit 28
+分子 #46: Mediator of RNA polymerase II transcription subunit 29
+分子 #47: Mediator of RNA polymerase II transcription subunit 30
+分子 #48: Mediator of RNA polymerase II transcription subunit 31
+分子 #49: Mediator of RNA polymerase II transcription subunit 1
+分子 #50: Mediator of RNA polymerase II transcription subunit 4
+分子 #51: Mediator of RNA polymerase II transcription subunit 6
+分子 #52: Mediator of RNA polymerase II transcription subunit 7
+分子 #53: Isoform 2 of Mediator of RNA polymerase II transcription subunit 8
+分子 #54: Mediator of RNA polymerase II transcription subunit 9
+分子 #55: Mediator of RNA polymerase II transcription subunit 10
+分子 #56: Mediator of RNA polymerase II transcription subunit 11
+分子 #57: Mediator of RNA polymerase II transcription subunit 14
+分子 #58: Mediator of RNA polymerase II transcription subunit 15
+分子 #59: Mediator of RNA polymerase II transcription subunit 17
+分子 #60: Mediator of RNA polymerase II transcription subunit 18
+分子 #61: Mediator of RNA polymerase II transcription subunit 19
+分子 #62: Mediator of RNA polymerase II transcription subunit 20
+分子 #63: Mediator of RNA polymerase II transcription subunit 21
+分子 #64: Mediator of RNA polymerase II transcription subunit 22
+分子 #65: Mediator of RNA polymerase II transcription subunit 26
+分子 #66: Mediator of RNA polymerase II transcription subunit 24
+分子 #67: Mediator of RNA polymerase II transcription subunit 23
+分子 #68: Isoform 2 of Mediator of RNA polymerase II transcription subunit 16
+分子 #69: DNA (69-MER)
+分子 #70: DNA(69-MER)
+分子 #71: ZINC ION
+分子 #72: MAGNESIUM ION
+分子 #73: IRON/SULFUR CLUSTER
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.9 |
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凍結 | 凍結剤: ETHANE |
-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 K2 SUMMIT (4k 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: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.07 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 48654 |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |