+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8480 | |||||||||
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タイトル | Cryo-EM map of the Mediator-RNAPII complex | |||||||||
マップデータ | Mediator-RNAPII complex | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / Formation of TC-NER Pre-Incision Complex / 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 / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape ...RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / Formation of TC-NER Pre-Incision Complex / 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 / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / regulation of septum digestion after cytokinesis / regulatory ncRNA-mediated heterochromatin formation / DNA-templated transcription elongation / core mediator complex / mediator complex / : / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / termination of RNA polymerase II transcription / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / tRNA transcription by RNA polymerase III / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / pericentric heterochromatin / RNA polymerase II, core complex / translation initiation factor binding / P-body / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / ユークロマチン / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / ポリメラーゼ / single-stranded DNA binding / transcription by RNA polymerase II / single-stranded RNA binding / nucleic acid binding / transcription coactivator activity / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleotide binding / クロマチン / 核小体 / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / metal ion binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Schizosaccharomyces pombe (分裂酵母) / Fission yeast (分裂酵母) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.8 Å | |||||||||
データ登録者 | Tsai K-L / Yu X / Gopalan S / Chao T-C / Zhang Y / Florens L / Washburn MP / Murakami K / Conaway RC / Conaway JW / Asturias F | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Nature / 年: 2017 タイトル: Mediator structure and rearrangements required for holoenzyme formation. 著者: Kuang-Lei Tsai / Xiaodi Yu / Sneha Gopalan / Ti-Chun Chao / Ying Zhang / Laurence Florens / Michael P Washburn / Kenji Murakami / Ronald C Conaway / Joan W Conaway / Francisco J Asturias / 要旨: The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is ...The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences transcription initiation and conveys regulatory information to the basal transcription machinery. Here we present a 4.4 Å resolution cryo-electron microscopy map of Schizosaccharomyces pombe Mediator in which conserved Mediator subunits are individually resolved. The essential Med14 subunit works as a central backbone that connects the Mediator head, middle and tail modules. Comparison with a 7.8 Å resolution cryo-electron microscopy map of a Mediator-RNA polymerase II holoenzyme reveals that changes in the structure of Med14 facilitate a large-scale Mediator rearrangement that is essential for holoenzyme formation. Our study suggests that access to different conformations and crosstalk between structural elements are essential for the Mediator regulation mechanism, and could explain the capacity of the complex to integrate multiple regulatory signals. | |||||||||
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_8480.map.gz | 19.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-8480-v30.xml emd-8480.xml | 43.3 KB 43.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_8480_fsc_1.xml emd_8480_fsc_2.xml | 6.3 KB 6.3 KB | 表示 表示 | FSCデータファイル |
画像 | emd_8480.png | 275.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8480 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8480 | 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_8480.map.gz / 形式: CCP4 / 大きさ: 20.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Mediator-RNAPII complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.62 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 : complex of Mediator and RNAPII
+超分子 #1: complex of Mediator and RNAPII
+分子 #1: Mediator complex subunit 6
+分子 #2: Mediator complex subunit 8
+分子 #3: Mediator complex subunit 17
+分子 #4: Mediator complex subunit 18
+分子 #5: Mediator complex subunit 20
+分子 #6: Mediator complex subunit 11
+分子 #7: Mediator complex subunit 22
+分子 #8: Mediator complex subunit 14
+分子 #9: Mediator complex subunit 4
+分子 #10: Mediator complex subunit 7
+分子 #11: Mediator complex subunit 21
+分子 #12: Mediator complex subunit 31
+分子 #13: Mediator complex subunit 27
+分子 #14: Mediator complex subunit 9
+分子 #15: Mediator complex subunit 19
+分子 #16: Mediator complex subunit 10
+分子 #17: RNA polymerase II subunit Rpb1
+分子 #18: RNA polymerase II subunit Rpb2
+分子 #19: RNA polymerase II subunit Rpb3
+分子 #20: RNA polymerase II subunit Rpb4
+分子 #21: RNA polymerase II subunit Rpb5
+分子 #22: RNA polymerase II subunit Rpb6
+分子 #23: RNA polymerase II subunit Rpb7
+分子 #24: RNA polymerase II subunit Rpb8
+分子 #25: RNA polymerase II subunit Rpb9
+分子 #26: RNA polymerase II subunit Rpb10
+分子 #27: RNA polymerase II subunit Rpb11
+分子 #28: RNA polymerase II subunit Rpb12
-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
濃度 | 1 mg/mL |
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緩衝液 | pH: 7.4 詳細: 20 mM HEPES, pH 7.4, 200 mM potassium acetate, 5 mM b-Mercaptoethanol, 0.01% NP-40 |
グリッド | モデル: C-flat-2/2 4C / 材質: COPPER / メッシュ: 400 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: HOMEMADE PLUNGER |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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: 100.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス(公称値): 4.0 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 22500 |
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 |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均露光時間: 7.0 sec. / 平均電子線量: 9.6 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |