+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23255 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Structure of the human Mediator-bound transcription pre-initiation complex | ||||||||||||||||||
マップデータ | |||||||||||||||||||
試料 |
| ||||||||||||||||||
キーワード | pre-initiation complex / Mediator / initiation / complex / transcription / TRANSCRIPTION-DNA complex | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 positive regulation of mediator complex assembly / positive regulation of T cell extravasation / LRR domain binding / negative regulation of smooth muscle cell differentiation / microfibril binding / RNA Polymerase III Chain Elongation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / RNA Polymerase III Transcription Termination / Cytosolic iron-sulfur cluster assembly ...positive regulation of mediator complex assembly / positive regulation of T cell extravasation / LRR domain binding / negative regulation of smooth muscle cell differentiation / microfibril binding / RNA Polymerase III Chain Elongation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / RNA Polymerase III Transcription Termination / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / regulation of transcription by RNA polymerase I / positive regulation of core promoter binding / RNA polymerase II core complex assembly / core mediator complex / positive regulation of mitotic recombination / meiotic sister chromatid cohesion / hair follicle maturation / RNA polymerase transcription factor SL1 complex / ventricular system development / snRNA transcription by RNA polymerase II / hair cell differentiation / RPAP3/R2TP/prefoldin-like complex / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / phosphatase activator activity / Cytosolic sensors of pathogen-associated DNA / nucleotide-excision repair, preincision complex assembly / 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 / RNA polymerase I core promoter sequence-specific DNA binding / TFIIF-class transcription factor complex binding / 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 / transcription factor TFIIF complex / DNA 5'-3' helicase / mediator complex / nuclear retinoic acid receptor binding / RNA Polymerase III Abortive And Retractive Initiation / adult heart development / Generic Transcription Pathway / transcription factor TFIIA complex / female germ cell nucleus / G protein-coupled receptor internalization / male pronucleus / female pronucleus / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of chromatin binding / RNA polymerase II general transcription initiation factor binding / germinal vesicle / nuclear vitamin D receptor binding / [RNA-polymerase]-subunit kinase / DNA 3'-5' helicase / limb development / RNA Polymerase I Transcription Termination / transcription preinitiation complex / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / MicroRNA (miRNA) biogenesis / cyclin-dependent protein serine/threonine kinase regulator activity / Signaling by FGFR2 IIIa TM / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / 3'-5' DNA helicase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / termination of RNA polymerase II transcription / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / cortical actin cytoskeleton / RNA polymerase II general transcription initiation factor activity / bone mineralization / cell division site / spinal cord development / mRNA Capping / protein acetylation / PIWI-interacting RNA (piRNA) biogenesis / RSV-host interactions / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / erythrocyte maturation 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.8 Å | ||||||||||||||||||
データ登録者 | Abdella R / Talyzina A | ||||||||||||||||||
資金援助 | 米国, 5件
| ||||||||||||||||||
引用 | ジャーナル: Science / 年: 2021 タイトル: Structure of the human Mediator-bound transcription preinitiation complex. 著者: R Abdella / A Talyzina / S Chen / C J Inouye / R Tjian / Y He / 要旨: Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is ...Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is recruited by transcription factors, facilitates the assembly of the PIC, and stimulates phosphorylation of the Pol II C-terminal domain (CTD) by the TFIIH subunit CDK7. Here, we present the cryo-electron microscopy structure of the human Mediator-bound PIC at a resolution below 4 angstroms. Transcription factor binding sites within Mediator are primarily flexibly tethered to the tail module. CDK7 is stabilized by multiple contacts with Mediator. Two binding sites exist for the Pol II CTD, one between the head and middle modules of Mediator and the other in the active site of CDK7, providing structural evidence for Pol II CTD phosphorylation within the Mediator-bound PIC. | ||||||||||||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_23255.map.gz | 254 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-23255-v30.xml emd-23255.xml | 91.9 KB 91.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_23255.png | 168.5 KB | ||
Filedesc metadata | emd-23255.cif.gz | 22.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23255 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23255 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_23255_validation.pdf.gz | 436.6 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_23255_full_validation.pdf.gz | 436.2 KB | 表示 | |
XML形式データ | emd_23255_validation.xml.gz | 7.1 KB | 表示 | |
CIF形式データ | emd_23255_validation.cif.gz | 8.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23255 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23255 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_23255.map.gz / 形式: CCP4 / 大きさ: 282.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
+全体 : Mediator-bound pre-initiation complex
+超分子 #1: Mediator-bound pre-initiation complex
+超分子 #2: RNA Polymerase II
+超分子 #3: Mediator
+超分子 #4: TFIIH
+超分子 #5: General transcription factors
+超分子 #6: promoter DNA
+超分子 #7: cyclin-H and associated factors
+分子 #1: Isoform 2 of Mediator of RNA polymerase II transcription subunit 16
+分子 #2: Mediator of RNA polymerase II transcription subunit 23
+分子 #3: Mediator of RNA polymerase II transcription subunit 24
+分子 #4: Mediator of RNA polymerase II transcription subunit 25
+分子 #5: DNA-directed RNA polymerase II subunit RPB1
+分子 #6: DNA-directed RNA polymerase II subunit RPB2
+分子 #7: DNA-directed RNA polymerase II subunit RPB3
+分子 #8: DNA-directed RNA polymerase II subunit RPB4
+分子 #9: DNA-directed RNA polymerase II subunit RPB5
+分子 #10: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #11: DNA-directed RNA polymerase II subunit RPB7
+分子 #12: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #13: DNA-directed RNA polymerase II subunit RPB9
+分子 #14: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #15: DNA-directed RNA polymerase II subunit RPB11-a
+分子 #16: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+分子 #17: Transcription initiation factor IIA subunit 1
+分子 #18: Transcription initiation factor IIA subunit 2
+分子 #19: Transcription initiation factor IIB
+分子 #20: TATA-box-binding protein
+分子 #21: General transcription factor IIE subunit 1
+分子 #22: Transcription initiation factor IIE subunit beta
+分子 #23: General transcription factor IIF subunit 1
+分子 #24: General transcription factor IIF subunit 2
+分子 #27: TFIIH basal transcription factor complex helicase XPB subunit
+分子 #28: TFIIH basal transcription factor complex helicase XPD subunit
+分子 #29: General transcription factor IIH subunit 1
+分子 #30: General transcription factor IIH subunit 4, p52
+分子 #31: General transcription factor IIH subunit 2
+分子 #32: General transcription factor IIH subunit 3
+分子 #33: General transcription factor IIH subunit 5
+分子 #34: CDK-activating kinase assembly factor MAT1
+分子 #35: Cyclin-dependent kinase 7
+分子 #36: Cyclin-H
+分子 #37: Mediator of RNA polymerase II transcription subunit 6
+分子 #38: Mediator of RNA polymerase II transcription subunit 8
+分子 #39: Mediator of RNA polymerase II transcription subunit 11
+分子 #40: Mediator of RNA polymerase II transcription subunit 17
+分子 #41: Mediator of RNA polymerase II transcription subunit 18
+分子 #42: Mediator of RNA polymerase II transcription subunit 20
+分子 #43: Mediator of RNA polymerase II transcription subunit 22
+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 14
+分子 #49: Mediator of RNA polymerase II transcription subunit 4
+分子 #50: Mediator of RNA polymerase II transcription subunit 7
+分子 #51: Mediator of RNA polymerase II transcription subunit 9
+分子 #52: Mediator of RNA polymerase II transcription subunit 10
+分子 #53: Mediator of RNA polymerase II transcription subunit 19
+分子 #54: Mediator of RNA polymerase II transcription subunit 21
+分子 #55: Mediator of RNA polymerase II transcription subunit 31
+分子 #56: Mediator of RNA polymerase II transcription subunit 15
+分子 #25: super core promoter sense strand
+分子 #26: super core promoter antisense strand
+分子 #57: MAGNESIUM ION
+分子 #58: ZINC ION
+分子 #59: IRON/SULFUR CLUSTER
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
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 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
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: 31.5 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
初期モデル | モデルのタイプ: OTHER |
---|---|
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 156383 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |