+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12614 | ||||||||||||||||||
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タイトル | XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3) | ||||||||||||||||||
マップデータ | Local resolution filtered and sharpened map | ||||||||||||||||||
試料 |
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キーワード | Initiation / TRANSCRIPTION | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 core TFIIH complex portion of holo TFIIH complex / nucleotide-excision repair, DNA duplex unwinding / hair cell differentiation / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / UV protection / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH core complex / transcription factor TFIIH holo complex ...core TFIIH complex portion of holo TFIIH complex / nucleotide-excision repair, DNA duplex unwinding / hair cell differentiation / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / UV protection / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / DNA 3'-5' helicase / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / 3'-5' DNA helicase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 I Transcription Initiation / ATPase activator activity / DNA topological change / RNA polymerase II transcribes snRNA genes / transcription-coupled nucleotide-excision repair / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / Formation of HIV-1 elongation complex containing HIV-1 Tat / embryonic organ development / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / response to UV / RNA Polymerase II Pre-transcription Events / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / isomerase activity / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / transcription elongation by RNA polymerase II / NoRC negatively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / cellular response to gamma radiation / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein localization / double-stranded DNA binding / response to oxidative stress / transcription by RNA polymerase II / damaged DNA binding / response to hypoxia / nuclear speck / positive regulation of apoptotic process / DNA repair / nucleolus / apoptotic process / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Homo sapiens (ヒト) / Human mastadenovirus C (ウイルス) | ||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.9 Å | ||||||||||||||||||
データ登録者 | Aibara S / Schilbach S | ||||||||||||||||||
資金援助 | ドイツ, 5件
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引用 | ジャーナル: Nature / 年: 2021 タイトル: Structures of mammalian RNA polymerase II pre-initiation complexes. 著者: Shintaro Aibara / Sandra Schilbach / Patrick Cramer / 要旨: The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) ...The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast and human PIC and a topological model for DNA opening by the general transcription factor TFIIH. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve the structure of TFIIH at 2.9-4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation. | ||||||||||||||||||
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_12614.map.gz | 285.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12614-v30.xml emd-12614.xml | 27 KB 27 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_12614_fsc.xml | 15.9 KB | 表示 | FSCデータファイル |
画像 | emd_12614.png | 151.1 KB | ||
マスクデータ | emd_12614_msk_1.map | 347.6 MB | マスクマップ | |
Filedesc metadata | emd-12614.cif.gz | 7.3 KB | ||
その他 | emd_12614_additional_1.map.gz emd_12614_half_map_1.map.gz emd_12614_half_map_2.map.gz | 203.4 MB 278.5 MB 278.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12614 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12614 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12614_validation.pdf.gz | 601.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12614_full_validation.pdf.gz | 601.4 KB | 表示 | |
XML形式データ | emd_12614_validation.xml.gz | 24 KB | 表示 | |
CIF形式データ | emd_12614_validation.cif.gz | 32.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12614 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12614 | HTTPS FTP |
-関連構造データ
関連構造データ | 7nvvMC 7nvrC 7nvsC 7nvtC 7nvuC 7nvwC 7nvxC 7nvyC 7nvzC 7nw0C 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 |
-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_12614.map.gz / 形式: CCP4 / 大きさ: 347.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Local resolution filtered and sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.05 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
-マスク #1
ファイル | emd_12614_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Local resolution filtered map, unsharpened
ファイル | emd_12614_additional_1.map | ||||||||||||
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注釈 | Local resolution filtered map, unsharpened | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Unfiltered half map 1
ファイル | emd_12614_half_map_1.map | ||||||||||||
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注釈 | Unfiltered 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: Unfiltered half map 2
ファイル | emd_12614_half_map_2.map | ||||||||||||
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注釈 | Unfiltered 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 : XPB-containing part of TFIIH
+超分子 #1: XPB-containing part of TFIIH
+分子 #1: General transcription factor IIH subunit 4
+分子 #2: General transcription factor IIH subunit 5
+分子 #3: General transcription and DNA repair factor IIH helicase subunit XPB
+分子 #6: General transcription factor IIE subunit 1
+分子 #7: Unassigned peptide, likely XPB
+分子 #8: Unassigned Peptide, likely TFIIE-Beta
+分子 #4: Non-template DNA
+分子 #5: Template DNA
+分子 #9: ADENOSINE-5'-DIPHOSPHATE
+分子 #10: MAGNESIUM ION
+分子 #11: BERYLLIUM TRIFLUORIDE 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: 7.5 |
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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: 43.0 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 |