+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12618 | ||||||||||||||||||
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タイトル | RNA polymerase II pre-initiation complex with closed promoter DNA in distal position | ||||||||||||||||||
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 MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / : / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / : / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / ventricular system development / hair follicle maturation / RNA polymerase transcription factor SL1 complex / hair cell differentiation / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / UV protection / transcription factor TFIIK complex / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA polymerase I core promoter sequence-specific DNA binding / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / transcription factor TFIIF complex / DNA 5'-3' helicase / RNA Polymerase III Abortive And Retractive Initiation / G protein-coupled receptor internalization / adult heart development / transcription factor TFIIA complex / female germ cell nucleus / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / male pronucleus / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / germinal vesicle / DNA 3'-5' helicase / transcription preinitiation complex / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / Signaling by FGFR2 IIIa TM / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIID complex / bone mineralization / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / organelle membrane / mRNA Capping / spinal cord development / protein acetylation / cell division site / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Homo sapiens (ヒト) / Sus scrofa (ブタ) / 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: 7.2 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_12618.map.gz | 320.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12618-v30.xml emd-12618.xml | 58.8 KB 58.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_12618_fsc.xml | 16.1 KB | 表示 | FSCデータファイル |
画像 | emd_12618.png | 147.5 KB | ||
マスクデータ | emd_12618_msk_1.map | 347.6 MB | マスクマップ | |
Filedesc metadata | emd-12618.cif.gz | 14.5 KB | ||
その他 | emd_12618_additional_1.map.gz emd_12618_half_map_1.map.gz emd_12618_half_map_2.map.gz | 204.7 MB 278 MB 278.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12618 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12618 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12618_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12618_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_12618_validation.xml.gz | 24 KB | 表示 | |
CIF形式データ | emd_12618_validation.cif.gz | 32.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12618 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12618 | HTTPS FTP |
-関連構造データ
関連構造データ | 7nvzMC 7nvrC 7nvsC 7nvtC 7nvuC 7nvvC 7nvwC 7nvxC 7nvyC 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_12618.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_12618_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_12618_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_12618_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_12618_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 : RNA polymerase II pre-initiation complex with closed promoter DNA...
+超分子 #1: RNA polymerase II pre-initiation complex with closed promoter DNA...
+分子 #1: TFIIH basal transcription factor complex helicase XPD subunit
+分子 #2: General transcription factor IIH subunit 1
+分子 #3: General transcription factor IIH subunit 4
+分子 #4: CDK-activating kinase assembly factor MAT1
+分子 #5: General transcription factor IIH subunit 3
+分子 #6: General transcription factor IIH subunit 5
+分子 #7: General transcription factor IIH subunit 2
+分子 #8: General transcription and DNA repair factor IIH helicase subunit XPB
+分子 #9: RPB1
+分子 #10: DNA-directed RNA polymerase subunit beta
+分子 #11: DNA-directed RNA polymerase II subunit RPB3
+分子 #12: RPOL4c domain-containing protein
+分子 #13: DNA-directed RNA polymerase II subunit E
+分子 #14: DNA-directed RNA polymerase II subunit F
+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: RNA_pol_L_2 domain-containing protein
+分子 #20: RNA polymerase II subunit K
+分子 #21: Transcription initiation factor IIB
+分子 #23: TATA-box-binding protein
+分子 #24: General transcription factor IIF subunit 1
+分子 #25: General transcription factor IIF subunit 2
+分子 #27: Transcription initiation factor IIA subunit 1
+分子 #28: Transcription initiation factor IIA subunit 2
+分子 #29: General transcription factor IIE subunit 1
+分子 #30: Transcription initiation factor IIE subunit beta
+分子 #31: Unassigned peptide, likely TFIIE-beta
+分子 #32: Unassigned peptide, likely XPB
+分子 #22: Non-template DNA
+分子 #26: Template DNA
+分子 #33: IRON/SULFUR CLUSTER
+分子 #34: ZINC ION
+分子 #35: 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: 7.5 |
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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: 41.1 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 |