+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-15135 | |||||||||
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タイトル | Human RNA polymerase I | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 RNA polymerase I transcription regulator complex / negative regulation of protein localization to nucleolus / nucleologenesis / neural crest formation / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / DNA/RNA hybrid binding / RPAP3/R2TP/prefoldin-like complex / RNA polymerase I general transcription initiation factor binding / regulation of transcription by RNA polymerase I ...RNA polymerase I transcription regulator complex / negative regulation of protein localization to nucleolus / nucleologenesis / neural crest formation / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / DNA/RNA hybrid binding / RPAP3/R2TP/prefoldin-like complex / RNA polymerase I general transcription initiation factor binding / regulation of transcription by RNA polymerase I / Cytosolic sensors of pathogen-associated DNA / 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 III Abortive And Retractive Initiation / RNA polymerase I preinitiation complex assembly / Abortive elongation of HIV-1 transcript in the absence of Tat / nucleobase-containing compound metabolic process / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / RNA Polymerase I Transcription Termination / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / PIWI-interacting RNA (piRNA) biogenesis / termination of RNA polymerase I transcription / 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 / mRNA Splicing - Minor Pathway / nucleolar large rRNA transcription by RNA polymerase I / RNA Polymerase I Transcription Initiation / transcription initiation at RNA polymerase I promoter / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / transcription by RNA polymerase I / rRNA transcription / transcription by RNA polymerase III / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase III activity / tRNA transcription by RNA polymerase III / RNA polymerase II, core complex / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA polymerase II activity / cell surface receptor protein tyrosine kinase signaling pathway / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / embryo implantation / mRNA Splicing - Major Pathway / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / protein-DNA complex / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / DNA-directed RNA polymerase / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome / single-stranded DNA binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / nucleic acid binding / protein stabilization / protein dimerization activity / chromatin binding / nucleolus / magnesium ion binding / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.09 Å | |||||||||
データ登録者 | Daiss JL / Pilsl M / Straub K / Bleckmann A / Hoecherl M / Heiss FB / Abascal-Palacios G / Ramsay E / Tluckova K / Mars JC ...Daiss JL / Pilsl M / Straub K / Bleckmann A / Hoecherl M / Heiss FB / Abascal-Palacios G / Ramsay E / Tluckova K / Mars JC / Fuertges T / Bruckmann A / Rudack T / Bernecky C / Lamour V / Panov K / Vannini A / Moss T / Engel C | |||||||||
資金援助 | ドイツ, 2件
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引用 | ジャーナル: Life Sci Alliance / 年: 2022 タイトル: The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. 著者: Julia L Daiß / Michael Pilsl / Kristina Straub / Andrea Bleckmann / Mona Höcherl / Florian B Heiss / Guillermo Abascal-Palacios / Ewan P Ramsay / Katarina Tlučková / Jean-Clement Mars / ...著者: Julia L Daiß / Michael Pilsl / Kristina Straub / Andrea Bleckmann / Mona Höcherl / Florian B Heiss / Guillermo Abascal-Palacios / Ewan P Ramsay / Katarina Tlučková / Jean-Clement Mars / Torben Fürtges / Astrid Bruckmann / Till Rudack / Carrie Bernecky / Valérie Lamour / Konstantin Panov / Alessandro Vannini / Tom Moss / Christoph Engel / 要旨: Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification ...Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk, and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This "dock II" domain resembles a truncated HMG box incapable of DNA binding which may serve as a downstream transcription factor-binding platform in metazoans. Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG box domain-containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_15135.map.gz | 2.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-15135-v30.xml emd-15135.xml | 30.1 KB 30.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_15135.png | 43.3 KB | ||
その他 | emd_15135_half_map_1.map.gz emd_15135_half_map_2.map.gz | 20 MB 20 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-15135 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15135 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_15135_validation.pdf.gz | 597.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_15135_full_validation.pdf.gz | 597.3 KB | 表示 | |
XML形式データ | emd_15135_validation.xml.gz | 10.2 KB | 表示 | |
CIF形式データ | emd_15135_validation.cif.gz | 12 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15135 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15135 | HTTPS FTP |
-関連構造データ
関連構造データ | 8a43MC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_15135.map.gz / 形式: CCP4 / 大きさ: 26.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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: 1.50846 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-ハーフマップ: #2
ファイル | emd_15135_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_15135_half_map_2.map | ||||||||||||
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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 I
+超分子 #1: RNA polymerase I
+分子 #1: DNA-directed RNA polymerase I subunit RPA1
+分子 #2: DNA-directed RNA polymerase I subunit RPA2
+分子 #3: DNA-directed RNA polymerases I and III subunit RPAC1
+分子 #4: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+分子 #5: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #6: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #7: DNA-directed RNA polymerase I subunit RPA12
+分子 #8: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #9: DNA-directed RNA polymerases I and III subunit RPAC2
+分子 #10: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+分子 #11: DNA-directed RNA polymerase I subunit RPA49
+分子 #12: DNA-directed RNA polymerase I subunit RPA34
-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: 7.8 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | JEOL CRYO ARM 200 |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 40.0 e/Å2 |
電子線 | 加速電圧: 200 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 / 最大 デフォーカス(公称値): 2.7 µm / 最小 デフォーカス(公称値): 1.2 µm |
-画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.09 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 108012 |
初期 角度割当 | タイプ: ANGULAR RECONSTITUTION |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION |