+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0092 | |||||||||
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タイトル | Structure of a yeast closed complex with distorted DNA (CCdist) | |||||||||
マップデータ | Locally filtered map | |||||||||
試料 |
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キーワード | rna polymerase ii / transcription initiation / promoter opening / TRANSCRIPTION | |||||||||
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) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.7 Å | |||||||||
データ登録者 | Dienemann C / Schwalb B | |||||||||
資金援助 | ドイツ, 2件
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引用 | ジャーナル: Mol Cell / 年: 2019 タイトル: Promoter Distortion and Opening in the RNA Polymerase II Cleft. 著者: Christian Dienemann / Björn Schwalb / Sandra Schilbach / Patrick Cramer / 要旨: Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron ...Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron microscopic (cryo-EM) structure of a yeast PIC that contains underwound, distorted promoter DNA in the closed Pol II cleft. The DNA duplex axis is offset at the upstream edge of the initially melted DNA region (IMR) where DNA opening begins. Unstable IMRs are found in a subset of yeast promoters that we show can still initiate transcription after depletion of the transcription factor (TF) IIH (TFIIH) translocase Ssl2 (XPB in human) from the nucleus in vivo. PIC-induced DNA distortions may thus prime the IMR for melting and may explain how unstable IMRs that are predicted in promoters of Pol I and Pol III can open spontaneously. These results suggest that DNA distortion in the polymerase cleft is a general mechanism that contributes to promoter opening. | |||||||||
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_0092.map.gz | 110.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0092-v30.xml emd-0092.xml | 68.2 KB 68.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0092.png | 157.1 KB | ||
Filedesc metadata | emd-0092.cif.gz | 14.9 KB | ||
その他 | emd_0092_half_map_1.map.gz emd_0092_half_map_2.map.gz | 128.9 MB 129.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0092 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0092 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0092_validation.pdf.gz | 385.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0092_full_validation.pdf.gz | 385.1 KB | 表示 | |
XML形式データ | emd_0092_validation.xml.gz | 12.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0092 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0092 | 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_0092.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 | Locally filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-ハーフマップ: Half map 1
ファイル | emd_0092_half_map_1.map | ||||||||||||
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注釈 | Half map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: half map 2
ファイル | emd_0092_half_map_2.map | ||||||||||||
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注釈 | half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : complex
+超分子 #1: complex
+超分子 #2: transcription factors
+超分子 #3: Polymerase
+超分子 #4: Nucleic acid
+超分子 #5: transcription factors
+分子 #1: General transcription and DNA repair factor IIH helicase subunit ...
+分子 #2: General transcription and DNA repair factor IIH subunit TFB1,Gene...
+分子 #3: General transcription and DNA repair factor IIH subunit TFB2,Gene...
+分子 #4: RNA polymerase II transcription factor B subunit 3
+分子 #5: General transcription and DNA repair factor IIH subunit TFB4,Gene...
+分子 #6: General transcription and DNA repair factor IIH subunit TFB5
+分子 #7: General transcription and DNA repair factor IIH subunit SSL1,Gene...
+分子 #8: General transcription and DNA repair factor IIH helicase subunit ...
+分子 #9: DNA-directed RNA polymerase II subunit RPB1
+分子 #10: DNA-directed RNA polymerase II subunit RPB2
+分子 #11: DNA-directed RNA polymerase II subunit RPB3
+分子 #12: DNA-directed RNA polymerase II subunit RPB4
+分子 #13: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+分子 #14: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #15: DNA-directed RNA polymerase II subunit RPB7
+分子 #16: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #17: DNA-directed RNA polymerase II subunit RPB9
+分子 #18: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #19: DNA-directed RNA polymerase II subunit RPB11
+分子 #20: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+分子 #21: Transcription initiation factor IIB
+分子 #22: TATA-box-binding protein
+分子 #23: Transcription initiation factor IIF subunit alpha
+分子 #24: Transcription initiation factor IIF subunit beta
+分子 #25: Transcription initiation factor IIA large subunit,Transcription i...
+分子 #26: Transcription initiation factor IIA subunit 2
+分子 #27: Transcription initiation factor IIE subunit alpha,Transcription i...
+分子 #28: Transcription initiation factor IIE subunit beta
+分子 #29: Unknown protein
+分子 #30: non-template DNA (HIS4)
+分子 #31: Template DNA (HIS4)
+分子 #32: IRON/SULFUR CLUSTER
+分子 #33: ZINC ION
+分子 #34: MAGNESIUM ION
-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
緩衝液 | pH: 7 |
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凍結 | 凍結剤: 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 QUANTUM (4k x 4k) 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: OTHER / 撮影モード: BRIGHT FIELD |
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: 6.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 60000 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |