+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23906 | ||||||||||||||||||
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タイトル | RNA polymerase II pre-initiation complex (PIC3) | ||||||||||||||||||
マップデータ | PIC3 | ||||||||||||||||||
試料 |
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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 / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / transcription open complex formation at RNA polymerase II promoter ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II core complex assembly / TFIIH-class transcription factor complex binding / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / transcription factor TFIIA complex / DNA 3'-5' helicase / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / transcription factor TFIIH holo complex / transcription preinitiation complex / DNA duplex unwinding / Processing of Capped Intron-Containing Pre-mRNA / poly(A)+ mRNA export from nucleus / 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 / 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 / RNA Polymerase II Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / protein phosphatase activator activity / 3'-5' DNA helicase activity / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Estrogen-dependent gene expression / ATPase activator activity / acetyltransferase activity / Dual incision in TC-NER / RNA polymerase II general transcription initiation factor activity / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase II activity / RNA polymerase II preinitiation complex assembly / DNA helicase activity / translation initiation factor binding / TBP-class protein binding / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / double-stranded DNA binding / DNA helicase / transcription by RNA polymerase II / nucleic acid binding / damaged DNA binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / ATP binding / nucleus / metal ion binding / cytosol 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / Baker's yeast (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: 3.4 Å | ||||||||||||||||||
データ登録者 | Yang C / Fujiwara R / Kim HJ / Gorbea Colon JJ / Steimle S / Garcia BA / Murakami K | ||||||||||||||||||
資金援助 | 米国, 5件
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引用 | ジャーナル: Mol Cell / 年: 2022 タイトル: Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. 著者: Chun Yang / Rina Fujiwara / Hee Jong Kim / Pratik Basnet / Yunye Zhu / Jose J Gorbea Colón / Stefan Steimle / Benjamin A Garcia / Craig D Kaplan / Kenji Murakami / 要旨: Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous ...Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation. | ||||||||||||||||||
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_23906.map.gz | 61.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-23906-v30.xml emd-23906.xml | 52.9 KB 52.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_23906_fsc.xml | 11.8 KB | 表示 | FSCデータファイル |
画像 | emd_23906.png | 40.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23906 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23906 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_23906_validation.pdf.gz | 350.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_23906_full_validation.pdf.gz | 349.9 KB | 表示 | |
XML形式データ | emd_23906_validation.xml.gz | 9.8 KB | 表示 | |
CIF形式データ | emd_23906_validation.cif.gz | 13.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23906 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23906 | HTTPS FTP |
-関連構造データ
関連構造データ | 7ml2MC 7meiC 7mk9C 7mkaC 7ml0C 7ml1C 7ml3C 7ml4C C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10865 (タイトル: Structural visualization of de novo initiation of RNA polymerase II transcription Data size: 14.3 TB Data #1: raw micrographs for PIC + ITC maps [micrographs - multiframe] Data #2: raw micrographs for EC+EC map [micrographs - multiframe]) |
-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_23906.map.gz / 形式: CCP4 / 大きさ: 361.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | PIC3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 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 : RNA polymerase II pre-initiation complex (PIC3)
+超分子 #1: RNA polymerase II pre-initiation complex (PIC3)
+超分子 #2: Pol II + TFIIB
+超分子 #3: DNA+TBP+TFIIA+TFIIE+TFIIF
+超分子 #4: TFIIH
+分子 #1: DNA-directed RNA polymerase subunit
+分子 #2: DNA-directed RNA polymerase subunit beta
+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 II subunit RPABC5
+分子 #11: DNA-directed RNA polymerase II subunit RPB11
+分子 #12: DNA-directed RNA polymerases II subunit RPABC4
+分子 #13: Transcription initiation factor IIB
+分子 #14: Transcription initiation factor IIF subunit alpha
+分子 #15: Transcription initiation factor IIF subunit beta
+分子 #16: Transcription initiation factor IIA large subunit
+分子 #17: Transcription initiation factor IIA subunit 2
+分子 #18: Transcription initiation factor IIE subunit alpha
+分子 #19: Transcription initiation factor IIE subunit beta
+分子 #22: BJ4_G0004860.mRNA.1.CDS.1
+分子 #23: Tfb1
+分子 #24: Tfb4
+分子 #25: General transcription and DNA repair factor IIH helicase subunit XPD
+分子 #26: General transcription and DNA repair factor IIH
+分子 #27: RNA polymerase II transcription factor B subunit 2
+分子 #28: General transcription and DNA repair factor IIH subunit TFB5
+分子 #29: General transcription and DNA repair factor IIH helicase subunit XPB
+分子 #30: BJ4_G0050160.mRNA.1.CDS.1
+分子 #20: template strand DNA
+分子 #21: non-template strand DNA
+分子 #31: ZINC ION
+分子 #32: MAGNESIUM ION
+分子 #33: 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
緩衝液 | pH: 7.6 |
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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 K3 BIOQUANTUM (6k x 4k) 平均電子線量: 45.0 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |