+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3846 | |||||||||||||||
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タイトル | STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH | |||||||||||||||
マップデータ | Transcription pre-initiation complex including Polymerase II and the transcription factors TBP, TFIIA, -B, -E, -F and -H | |||||||||||||||
試料 |
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キーワード | transcription initiation / TRANSCRIPTION / macromolecular complex | |||||||||||||||
機能・相同性 | 機能・相同性情報 regulation of mitotic recombination / RNA polymerase II promoter clearance / 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 / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / regulation of transcription by RNA polymerase III ...regulation of mitotic recombination / RNA polymerase II promoter clearance / 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 / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / RPB4-RPB7 complex / DNA 5'-3' helicase / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 3'-5' helicase / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA binding, bending / RNA Polymerase I Transcription Initiation / DNA duplex unwinding / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / 3'-5' DNA helicase activity / 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 / ATPase activator activity / 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 / ATP-dependent activity, acting on DNA / 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 / transcription coregulator activity / translation initiation factor binding / TBP-class protein binding / DNA helicase activity / isomerase activity / DNA-templated transcription initiation / nucleotide-excision repair / 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 類似検索 - 分子機能 | |||||||||||||||
生物種 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) / 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: 4.7 Å | |||||||||||||||
データ登録者 | Schilbach S / Hantsche M / Tegunov D / Dienemann C / Wigge C / Urlaub H / Cramer P | |||||||||||||||
資金援助 | ドイツ, 4件
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引用 | ジャーナル: Nature / 年: 2017 タイトル: Structures of transcription pre-initiation complex with TFIIH and Mediator. 著者: S Schilbach / M Hantsche / D Tegunov / C Dienemann / C Wigge / H Urlaub / P Cramer / 要旨: For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron ...For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II. | |||||||||||||||
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_3846.map.gz | 151.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3846-v30.xml emd-3846.xml | 66.6 KB 66.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_3846.png | 173.8 KB | ||
Filedesc metadata | emd-3846.cif.gz | 15.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3846 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3846 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_3846_validation.pdf.gz | 222.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_3846_full_validation.pdf.gz | 222 KB | 表示 | |
XML形式データ | emd_3846_validation.xml.gz | 6.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3846 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3846 | 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_3846.map.gz / 形式: CCP4 / 大きさ: 163.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Transcription pre-initiation complex including Polymerase II and the transcription factors TBP, TFIIA, -B, -E, -F and -H | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.37 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 : Pre-Initiation Complex (PIC)
+超分子 #1: Pre-Initiation Complex (PIC)
+超分子 #2: Polymerase
+超分子 #3: initiation factors
+超分子 #4: Transcription factors
+超分子 #5: nucleic acid
+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 RPABC1
+分子 #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #7: DNA-directed RNA polymerase II subunit RPB7
+分子 #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #9: DNA-directed RNA polymerase II subunit RPB9
+分子 #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #11: DNA-directed RNA polymerase II subunit RPB11
+分子 #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+分子 #13: Transcription initiation factor IIB
+分子 #15: TATA-box-binding protein
+分子 #16: Transcription initiation factor IIF subunit alpha
+分子 #17: Transcription initiation factor IIF subunit beta
+分子 #19: Transcription initiation factor IIA large subunit
+分子 #20: Transcription initiation factor IIA subunit 2
+分子 #21: Transcription initiation factor IIE subunit alpha
+分子 #22: Transcription initiation factor IIE subunit beta
+分子 #23: DNA repair helicase RAD3
+分子 #24: RNA polymerase II transcription factor B subunit 1
+分子 #25: RNA polymerase II transcription factor B subunit 2
+分子 #26: RNA polymerase II transcription factor B subunit 3
+分子 #27: RNA polymerase II transcription factor B subunit 4
+分子 #28: RNA polymerase II transcription factor B subunit 5
+分子 #29: Suppressor of stem-loop protein 1
+分子 #30: DNA repair helicase RAD25
+分子 #31: Unknown protein
+分子 #14: NONTEMPLATE DNA
+分子 #18: TEMPLATE DNA
+分子 #32: ZINC ION
+分子 #33: MAGNESIUM ION
+分子 #34: IRON/SULFUR CLUSTER
-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 | 0.70 mg/mL |
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緩衝液 | pH: 7.6 |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD 詳細: QUANTIFOIL HOLEY GOLD GRIDS WERE GLOW-DISCHARGED BEFORE DEPOSITION OF SAMPLE. |
凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK IV 詳細: GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 / 撮影したグリッド数: 3 / 実像数: 13000 / 平均露光時間: 10.0 sec. / 平均電子線量: 42.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 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): 0.5 µm / 倍率(公称値): 105000 |
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: EMDB MAP |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 58000 |
初期 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION (ver. 2.0.4) |
最終 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION (ver. 2.0.4) |
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: OTHER |
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得られたモデル | PDB-5oqj: |