+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8t1i | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Atomic model of the mammalian Mediator complex with MED26 subunit | |||||||||
要素 |
| |||||||||
キーワード | GENE REGULATION / mouse mediator / complex / MED26 subunit | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of T cell extravasation / Nuclear Receptor transcription pathway / 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 T cell extravasation / Nuclear Receptor transcription pathway / 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 / Regulation of lipid metabolism by PPARalpha / core mediator complex / regulation of vitamin D receptor signaling pathway / Cytoprotection by HMOX1 / Estrogen-dependent gene expression / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / nuclear retinoic acid receptor binding / mediator complex / positive regulation of keratinocyte differentiation / embryonic heart tube development / camera-type eye development / cellular response to thyroid hormone stimulus / positive regulation of hepatocyte proliferation / embryonic hindlimb morphogenesis / nuclear vitamin D receptor binding / peroxisome proliferator activated receptor binding / limb development / lens development in camera-type eye / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / nuclear thyroid hormone receptor binding / mammary gland epithelial cell proliferation / megakaryocyte development / histone acetyltransferase binding / cellular response to hepatocyte growth factor stimulus / cortical actin cytoskeleton / termination of RNA polymerase II transcription / LBD domain binding / 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 / monocyte differentiation / blastocyst development / general transcription initiation factor binding / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of fibroblast proliferation / ubiquitin ligase complex / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / cellular response to epidermal growth factor stimulus / peroxisome proliferator activated receptor signaling pathway / lactation / positive regulation of erythrocyte differentiation / nuclear receptor coactivator activity / liver development / promoter-specific chromatin binding / nuclear estrogen receptor binding / nuclear receptor binding / protein-DNA complex / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / animal organ morphogenesis / mRNA transcription by RNA polymerase II / cell morphogenesis / brain development / chromatin DNA binding / transcription coactivator binding / protein import into nucleus / transcription corepressor activity / ubiquitin protein ligase activity / heart development / actin binding / angiogenesis / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / cytoskeleton / nuclear body / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / positive regulation of cell population proliferation / positive regulation of gene expression / protein-containing complex binding 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.68 Å | |||||||||
データ登録者 | Zhao, H. / Asturias, F. | |||||||||
資金援助 | 米国, 2件
| |||||||||
引用 | ジャーナル: Mol Cell / 年: 2024 タイトル: An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II. 著者: Haiyan Zhao / Jiaqin Li / Yufei Xiang / Sohail Malik / Supriya V Vartak / Giovana M B Veronezi / Natalie Young / McKayla Riney / Jens Kalchschmidt / Andrea Conte / Seol Kyoung Jung / Srinivas ...著者: Haiyan Zhao / Jiaqin Li / Yufei Xiang / Sohail Malik / Supriya V Vartak / Giovana M B Veronezi / Natalie Young / McKayla Riney / Jens Kalchschmidt / Andrea Conte / Seol Kyoung Jung / Srinivas Ramachandran / Robert G Roeder / Yi Shi / Rafael Casellas / Francisco J Asturias / 要旨: The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent ...The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent transcription remains unknown. We investigated modulation of metazoan MED interaction with RNA polymerase II (RNA Pol II) by antagonistic effects of the MED26 subunit and the CDK8 kinase module (CKM). Biochemical analysis of CKM-MED showed that the CKM blocks binding of the RNA Pol II carboxy-terminal domain (CTD), preventing RNA Pol II interaction. This restriction is eliminated by nuclear receptor (NR) binding to CKM-MED, which enables CTD binding in a MED26-dependent manner. Cryoelectron microscopy (cryo-EM) and crosslinking-mass spectrometry (XL-MS) revealed that the structural basis for modulation of CTD interaction with MED relates to a large intrinsically disordered region (IDR) in CKM subunit MED13 that blocks MED26 and CTD interaction with MED but is repositioned upon NR binding. Hence, NRs can control transcription initiation by priming CKM-MED for MED26-dependent RNA Pol II interaction. | |||||||||
履歴 |
|
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
---|
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8t1i.cif.gz | 1.3 MB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb8t1i.ent.gz | 956.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8t1i.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8t1i_validation.pdf.gz | 1.5 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 8t1i_full_validation.pdf.gz | 1.6 MB | 表示 | |
XML形式データ | 8t1i_validation.xml.gz | 192.3 KB | 表示 | |
CIF形式データ | 8t1i_validation.cif.gz | 313.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/t1/8t1i ftp://data.pdbj.org/pub/pdb/validation_reports/t1/8t1i | HTTPS FTP |
-関連構造データ
関連構造データ | 40968MC 8t9dC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
---|---|
類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
+Mediator of RNA polymerase II transcription subunit ... , 26種, 26分子 ABCDEFGHIJKLMNOPQRSTUVWXYZ
-タンパク質・ペプチド , 1種, 1分子 a
#27: タンパク質・ペプチド | 分子量: 1720.111 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Mouse mediator complex / タイプ: COMPLEX / Entity ID: all / 由来: NATURAL |
---|---|
分子量 | 値: 1.0 MDa / 実験値: NO |
由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
緩衝液 | pH: 7.9 |
試料 | 濃度: 0.1 mg/ml / 包埋: YES / シャドウイング: NO / 染色: NO / 凍結: YES |
EM embedding | Material: ice |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
-電子顕微鏡撮影
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TALOS ARCTICA |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3500 nm / 最小 デフォーカス(公称値): 700 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm |
撮影 | 電子線照射量: 22.5 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
EMソフトウェア | 名称: PHENIX / バージョン: dev_3758: / カテゴリ: モデル精密化 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
3次元再構成 | 解像度: 4.68 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 199078 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
|