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万見- EMDB-31191: Human Mediator (deletion of MED1-IDR) in a Tail-extended conformation -
+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-31191 | |||||||||
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タイトル | Human Mediator (deletion of MED1-IDR) in a Tail-extended conformation | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Mediator complex / TRANSCRIPTION | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of mediator complex assembly / positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / mammary gland branching involved in thelarche ...positive regulation of mediator complex assembly / positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / mammary gland branching involved in thelarche / G0 to G1 transition / thyroid hormone receptor signaling pathway / core mediator complex / regulation of vitamin D receptor signaling pathway / LBD domain binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / mediator complex / nuclear retinoic acid receptor binding / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / cellular response to thyroid hormone stimulus / monocyte differentiation / positive regulation of hepatocyte proliferation / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / nuclear vitamin D receptor binding / positive regulation of chromatin binding / limb development / lens development in camera-type eye / nuclear thyroid hormone receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / embryonic placenta development / megakaryocyte development / cellular response to steroid hormone stimulus / histone acetyltransferase binding / cellular response to hepatocyte growth factor stimulus / termination of RNA polymerase II transcription / cortical actin cytoskeleton / RSV-host interactions / epithelial cell proliferation involved in mammary gland duct elongation / fat cell differentiation / skeletal muscle cell differentiation / mammary gland branching involved in pregnancy / somatic stem cell population maintenance / nuclear retinoid X receptor binding / blastocyst development / general transcription initiation factor binding / cellular response to epidermal growth factor stimulus / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / peroxisome proliferator activated receptor signaling pathway / animal organ regeneration / erythrocyte development / positive regulation of transcription elongation by RNA polymerase II / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / negative regulation of fibroblast proliferation / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / transcription coregulator activity / RORA activates gene expression / lactation / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of erythrocyte differentiation / Activation of gene expression by SREBF (SREBP) / liver development / nuclear receptor coactivator activity / mRNA transcription by RNA polymerase II / nuclear receptor binding / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / PPARA activates gene expression / Heme signaling / Nuclear Receptor transcription pathway / brain development / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / chromatin DNA binding / transcription coactivator binding / DNA-directed 5'-3' RNA polymerase activity / protein import into nucleus / transcription corepressor activity / ubiquitin protein ligase activity / Circadian Clock / actin binding / DNA-binding transcription factor binding / transcription regulator complex / angiogenesis / Estrogen-dependent gene expression / transcription coactivator activity / transcription by RNA polymerase II 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: 3.5 Å | |||||||||
データ登録者 | Yin X / Li J | |||||||||
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_31191.map.gz | 33.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-31191-v30.xml emd-31191.xml | 49.9 KB 49.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_31191.png | 109.3 KB | ||
Filedesc metadata | emd-31191.cif.gz | 14.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-31191 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31191 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_31191_validation.pdf.gz | 361.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_31191_full_validation.pdf.gz | 360.9 KB | 表示 | |
XML形式データ | emd_31191_validation.xml.gz | 7.8 KB | 表示 | |
CIF形式データ | emd_31191_validation.cif.gz | 9.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31191 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31191 | 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_31191.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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ボクセルのサイズ | X=Y=Z: 1.054 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
-試料の構成要素
+全体 : Structure of the human Mediator complex
+超分子 #1: Structure of the human Mediator complex
+分子 #1: Mediator of RNA polymerase II transcription subunit 1
+分子 #2: Unknown Chain (poly A)
+分子 #3: Mediator of RNA polymerase II transcription subunit 4
+分子 #4: Mediator of RNA polymerase II transcription subunit 6
+分子 #5: Mediator of RNA polymerase II transcription subunit 7
+分子 #6: Isoform 2 of Mediator of RNA polymerase II transcription subunit 8
+分子 #7: Mediator of RNA polymerase II transcription subunit 9
+分子 #8: Mediator of RNA polymerase II transcription subunit 10
+分子 #9: Mediator of RNA polymerase II transcription subunit 11
+分子 #10: Mediator of RNA polymerase II transcription subunit 14
+分子 #11: Mediator of RNA polymerase II transcription subunit 15
+分子 #12: Isoform 2 of Mediator of RNA polymerase II transcription subunit 16
+分子 #13: Mediator of RNA polymerase II transcription subunit 17
+分子 #14: Mediator of RNA polymerase II transcription subunit 18
+分子 #15: Mediator of RNA polymerase II transcription subunit 19
+分子 #16: Mediator of RNA polymerase II transcription subunit 20
+分子 #17: Mediator of RNA polymerase II transcription subunit 21
+分子 #18: Mediator of RNA polymerase II transcription subunit 22
+分子 #19: Mediator of RNA polymerase II transcription subunit 23
+分子 #20: Mediator of RNA polymerase II transcription subunit 24
+分子 #21: Mediator of RNA polymerase II transcription subunit 25
+分子 #22: Mediator of RNA polymerase II transcription subunit 26
+分子 #23: Mediator of RNA polymerase II transcription subunit 27
+分子 #24: Mediator of RNA polymerase II transcription subunit 28
+分子 #25: Mediator of RNA polymerase II transcription subunit 29
+分子 #26: Mediator of RNA polymerase II transcription subunit 30
+分子 #27: Mediator of RNA polymerase II transcription subunit 31
+分子 #28: ZINC 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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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: 8 |
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: PLASMA CLEANING |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 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 | C2レンズ絞り径: 70.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
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 |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 95433 |
初期 角度割当 | タイプ: OTHER |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: AB INITIO MODEL |
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得られたモデル | PDB-7emf: |