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基本情報
登録情報 | データベース: EMDB / ID: EMD-12795 | |||||||||
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タイトル | Cryo-EM structure of human RNA Polymerase I in elongation state | |||||||||
![]() | Elongating human RNA Polymerase I, Map A, unsharpened | |||||||||
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![]() | RNA polymerase I / human / rRNA transcription / DNA-dependent RNA polymerase / elongation state / TRANSCRIPTION | |||||||||
機能・相同性 | ![]() 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 / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / RNA polymerase II activity / Formation of RNA Pol II elongation complex / 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 / cellular response to leukemia inhibitory factor / DNA-templated transcription initiation / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / 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) / ribonucleoside binding / Formation of TC-NER Pre-Incision Complex / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / 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 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.7 Å | |||||||||
![]() | Misiaszek AD / Girbig M | |||||||||
![]() | ![]() タイトル: Cryo-EM structures of human RNA polymerase I. 著者: Agata D Misiaszek / Mathias Girbig / Helga Grötsch / Florence Baudin / Brice Murciano / Aleix Lafita / Christoph W Müller / ![]() ![]() 要旨: RNA polymerase I (Pol I) specifically synthesizes ribosomal RNA. Pol I upregulation is linked to cancer, while mutations in the Pol I machinery lead to developmental disorders. Here we report the ...RNA polymerase I (Pol I) specifically synthesizes ribosomal RNA. Pol I upregulation is linked to cancer, while mutations in the Pol I machinery lead to developmental disorders. Here we report the cryo-EM structure of elongating human Pol I at 2.7 Å resolution. In the exit tunnel, we observe a double-stranded RNA helix that may support Pol I processivity. Our structure confirms that human Pol I consists of 13 subunits with only one subunit forming the Pol I stalk. Additionally, the structure of human Pol I in complex with the initiation factor RRN3 at 3.1 Å resolution reveals stalk flipping upon RRN3 binding. We also observe an inactivated state of human Pol I bound to an open DNA scaffold at 3.3 Å resolution. Lastly, the high-resolution structure of human Pol I allows mapping of disease-related mutations that can aid understanding of disease etiology. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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 | ![]() | 65.2 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 61.1 KB 61.1 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 10 KB | 表示 | ![]() |
画像 | ![]() | 62.1 KB | ||
マスクデータ | ![]() ![]() ![]() | 83.7 MB 83.7 MB 83.7 MB | ![]() | |
Filedesc metadata | ![]() | 11.5 KB | ||
その他 | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 75.3 MB 64.9 MB 73.5 MB 66.8 MB 62.3 MB 73.9 MB 76.1 MB 67.2 MB 74.8 MB 65.4 MB 65.4 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1.1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.1 MB | 表示 | |
XML形式データ | ![]() | 17 KB | 表示 | |
CIF形式データ | ![]() | 22.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7ob9MC ![]() 7obaC ![]() 7obbC 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 ( |
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類似構造データ | |
電子顕微鏡画像生データ | ![]() Data size: 1.8 TB Data #1: Unaligned multi-frame micrographs of human RNA polymerase I in elongating state [micrographs - multiframe]) |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Elongating human RNA Polymerase I, Map A, unsharpened | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.822 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
+マスク #2
+マスク #3
+追加マップ: Elongating human RNA Polymerase I, Map B1, RELION...
+追加マップ: Elongating human RNA Polymerase I, Map A, locally...
+追加マップ: Elongating human RNA Polymerase I, Map B, RELION...
+追加マップ: Elongating human RNA Polymerase I, Map B2, RELION...
+追加マップ: Elongating human RNA Polymerase I, Map B1, RELION...
+追加マップ: Elongating human RNA Polymerase I, Map B, RELION...
+追加マップ: Elongating human RNA Polymerase I, Map B2, RELION...
+追加マップ: Elongating human RNA Polymerase I, Map C, Phenix...
+追加マップ: Elongating human RNA Polymerase I, Map C, Phenix...
+ハーフマップ: Elongating human RNA Polymerase I, Map A, half map 2
+ハーフマップ: Elongating human RNA Polymerase I, Map A, half map 2
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試料の構成要素
+全体 : RNA polymerase I
+超分子 #1: RNA polymerase I
+超分子 #2: RNA polymerase I
+超分子 #3: RNA and DNA
+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 polymerase I subunit RPA43
+分子 #7: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #8: DNA-directed RNA polymerase I subunit RPA12
+分子 #9: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #10: DNA-directed RNA polymerases I and III subunit RPAC2
+分子 #11: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+分子 #12: DNA-directed RNA polymerase I subunit RPA34
+分子 #13: DNA-directed RNA polymerase I subunit RPA49
+分子 #14: RNA
+分子 #15: DNA non-template strand
+分子 #16: DNA template strand
+分子 #17: ZINC ION
+分子 #18: 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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.7 mg/mL | |||||||||||||||
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緩衝液 | pH: 7.5 構成要素:
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グリッド | モデル: Quantifoil R2/1 / 材質: COPPER / メッシュ: 200 / 前処理 - タイプ: PLASMA CLEANING / 前処理 - 時間: 30 sec. / 前処理 - 雰囲気: OTHER 詳細: NanoClean plasma cleaner (Fischione Instruments, Model 1070) | |||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 288 K / 装置: FEI VITROBOT MARK IV / 詳細: blot force 3, blot time 0 s, wait time 0 s. | |||||||||||||||
詳細 | Human RNA Polymerase I with 1.5 molar excess of the synthetic nucleic acid template |
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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 (6k x 4k) / 撮影したグリッド数: 1 / 実像数: 10053 / 平均電子線量: 50.9 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 100.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 105000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
初期モデル |
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詳細 | Initial rigid body fitting with UCSF Chimera followed by manual model fitting in Coot. | ||||||||||||||||
得られたモデル | ![]() PDB-7ob9: |