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- EMDB-3383: Transcription initiation complex structures elucidate DNA opening (CC) -
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基本情報
登録情報 | データベース: EMDB / ID: EMD-3383 | |||||||||
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タイトル | Transcription initiation complex structures elucidate DNA opening (CC) | |||||||||
![]() | sharpened CC map | |||||||||
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![]() | Gene expression / Transcription initiation | |||||||||
機能・相同性 | ![]() 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 factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding ...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 factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / 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 / protein phosphatase activator activity / 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 / positive regulation of transcription initiation by RNA polymerase II / 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 / 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 / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / transcription coregulator activity / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / negative regulation of DNA-templated transcription / mRNA binding / chromatin binding / regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 8.8 Å | |||||||||
![]() | Plaschka C / Hantsche M / Dienemann C / Burzinski C / Plitzko J / Cramer P | |||||||||
![]() | ![]() タイトル: Transcription initiation complex structures elucidate DNA opening. 著者: C Plaschka / M Hantsche / C Dienemann / C Burzinski / J Plitzko / P Cramer / ![]() 要旨: Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) ...Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 94.2 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 14.2 KB 14.2 KB | 表示 表示 | ![]() |
画像 | ![]() | 108.9 KB | ||
その他 | ![]() | 92.8 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 5fz5MC ![]() 3375C ![]() 3376C ![]() 3377C ![]() 3378C ![]() 3379C ![]() 3380C ![]() 3381C ![]() 3382C ![]() 5fywC ![]() 5ip7C ![]() 5ip9C M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | sharpened CC map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-添付マップデータ: emd 3383 additional 1.map
ファイル | emd_3383_additional_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
-全体 : yeast Pol II transcription initiation complex (closed DNA)
全体 | 名称: yeast Pol II transcription initiation complex (closed DNA) |
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要素 |
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-超分子 #1000: yeast Pol II transcription initiation complex (closed DNA)
超分子 | 名称: yeast Pol II transcription initiation complex (closed DNA) タイプ: sample / ID: 1000 / 集合状態: Monomer / Number unique components: 7 |
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分子量 | 理論値: 890 KDa |
-分子 #1: DNA-directed RNA polymerase II
分子 | 名称: DNA-directed RNA polymerase II / タイプ: protein_or_peptide / ID: 1 / Name.synonym: RNA polymerase II / コピー数: 1 / 組換発現: No |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 513 KDa |
-分子 #2: Transcription Factor IIA
分子 | 名称: Transcription Factor IIA / タイプ: protein_or_peptide / ID: 2 / Name.synonym: TFIIA / コピー数: 1 / 組換発現: Yes |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 45 KDa |
組換発現 | 生物種: ![]() ![]() |
-分子 #3: Transcription Factor IIB
分子 | 名称: Transcription Factor IIB / タイプ: protein_or_peptide / ID: 3 / Name.synonym: TFIIB / コピー数: 1 / 組換発現: Yes |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 38 KDa |
組換発現 | 生物種: ![]() ![]() |
-分子 #4: TATA-box-binding protein
分子 | 名称: TATA-box-binding protein / タイプ: protein_or_peptide / ID: 4 / Name.synonym: TBP, SPT15 / コピー数: 1 / 組換発現: Yes |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 27 KDa |
組換発現 | 生物種: ![]() ![]() |
-分子 #5: Transcription Factor IIE
分子 | 名称: Transcription Factor IIE / タイプ: protein_or_peptide / ID: 5 / Name.synonym: TFIIE / コピー数: 1 / 組換発現: Yes |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 91 KDa |
組換発現 | 生物種: ![]() ![]() |
-分子 #6: Transcription Factor IIF
分子 | 名称: Transcription Factor IIF / タイプ: protein_or_peptide / ID: 6 / Name.synonym: TFIIF / コピー数: 1 / 組換発現: Yes |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 129 KDa |
組換発現 | 生物種: ![]() ![]() |
-分子 #7: synthetic promoter DNA construct (closed)
分子 | 名称: synthetic promoter DNA construct (closed) / タイプ: dna / ID: 7 / 詳細: double-stranded closed promoter DNA / 分類: DNA / Structure: DOUBLE HELIX / Synthetic?: Yes |
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由来(天然) | 生物種: unidentified (未定義) |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.3 mg/mL |
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緩衝液 | pH: 7.5 詳細: 25 mM HEPES-KOH pH 7.5, 150 mM potassium acetate, 2 mM MgCl2, 5 mM DTT |
グリッド | 詳細: R3.5/1 holey carbon grids (Quantifoil) |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK IV 手法: Quantifoil R 3.5/1 holey carbon grids were glow-discharged before deposition of 4.5 microliters of sample. Grids were then blotted for 8.5 s and plunge-frozen in liquid ethane. |
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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 - 名称: GIF Quantum エネルギーフィルター - エネルギー下限: 0.0 eV エネルギーフィルター - エネルギー上限: 20.0 eV |
日付 | 2016年6月20日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 実像数: 959 / 平均電子線量: 40 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 37037 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 5.0 µm / 最小 デフォーカス(公称値): 0.8 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 |
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画像解析
CTF補正 | 詳細: Each particle |
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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: 8.8 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: RELION / 使用した粒子像数: 5690 |