+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2785 | |||||||||
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タイトル | Architecture of the RNA polymerase II-Mediator core transcription initiation complex | |||||||||
マップデータ | cITC | |||||||||
試料 |
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キーワード | transcription / transcription initiation / RNA polymerase II / General Transcription Factors | |||||||||
機能・相同性 | 機能・相同性情報 RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / transcription open complex formation at RNA polymerase II promoter / RPB4-RPB7 complex / transcriptional start site selection at RNA polymerase II promoter ...RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / transcription open complex formation at RNA polymerase II promoter / RPB4-RPB7 complex / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA binding, bending / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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 / transcription factor TFIID complex / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translesion synthesis / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing / disordered domain specific binding / ribosome biogenesis / peroxisome / single-stranded DNA binding / DNA-binding transcription factor binding / transcription regulator complex / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / negative regulation of DNA-templated transcription / chromatin binding / mRNA binding / nucleotide binding / regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / Saccharomyces mikatae (酵母) / synthetic construct (人工物) | |||||||||
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 | Plaschka C / Lariviere L / Wenzeck L / Hemann M / Tegunov D / Petrotchenko EV / Borchers CH / Baumeister W / Herzog F / Villa E / Cramer P | |||||||||
引用 | ジャーナル: Nature / 年: 2015 タイトル: Architecture of the RNA polymerase II-Mediator core initiation complex. 著者: C Plaschka / L Larivière / L Wenzeck / M Seizl / M Hemann / D Tegunov / E V Petrotchenko / C H Borchers / W Baumeister / F Herzog / E Villa / P Cramer / 要旨: The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all ...The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7 Å resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation. | |||||||||
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_2785.map.gz | 77.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-2785-v30.xml emd-2785.xml | 25.6 KB 25.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_2785.png | 100.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2785 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2785 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_2785_validation.pdf.gz | 231.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_2785_full_validation.pdf.gz | 230.3 KB | 表示 | |
XML形式データ | emd_2785_validation.xml.gz | 6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2785 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2785 | 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_2785.map.gz / 形式: CCP4 / 大きさ: 81.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | cITC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.35 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 : cITC
+超分子 #1000: cITC
+分子 #1: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
+分子 #2: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
+分子 #3: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
+分子 #4: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
+分子 #5: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
+分子 #6: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
+分子 #7: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
+分子 #8: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
+分子 #9: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
+分子 #10: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
+分子 #11: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
+分子 #12: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
+分子 #13: TRANSCRIPTION INITIATION FACTOR IIB
+分子 #14: TATA-box-binding protein
+分子 #15: Transcription initiation factor IIF subunit alpha
+分子 #16: Transcription initiation factor IIF subunit beta
+分子 #17: template DNA
+分子 #18: nontemplate DNA
+分子 #19: RNA
-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 | 0.15 mg/mL |
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緩衝液 | pH: 7.5 詳細: 25 mM HEPES-KOH pH 7.5, 180 mM Potassium acetate, 5 % Glycerol, 5 mM DTT |
凍結 | 凍結剤: ETHANE / 装置: OTHER 手法: Grids were glow-discharged for 20 s before deposition of 4 microliters sample and incubated for 30 s. Grids were washed twice with 4 microliters distilled water, blotted, and then vitrified. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | カテゴリ: CCD / フィルム・検出器のモデル: GATAN K2 (4k x 4k) / 実像数: 2972 / 平均電子線量: 25 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 37169 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2 mm / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 37000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
詳細 | Particles were picked using EMAN2 and were processed using RELION 1.2. |
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CTF補正 | 詳細: Each particle |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 7.8 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: RELION, 1.2 詳細: The density was filtered according to local resolution and further a temperature factor of minus 340 A2 was applied. 使用した粒子像数: 4439 |