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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-4364 | |||||||||
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タイトル | Prespliceosome structure provides insight into spliceosome assembly and regulation (map A2) | |||||||||
![]() | Sharpened A2 map | |||||||||
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機能・相同性 | ![]() positive regulation of RNA binding / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / poly(U) RNA binding ...positive regulation of RNA binding / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / poly(U) RNA binding / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome assembly / U4 snRNP / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / U1 snRNP / pre-mRNA 5'-splice site binding / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / regulation of alternative mRNA splicing, via spliceosome / mRNA 5'-splice site recognition / regulation of RNA splicing / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / response to xenobiotic stimulus / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytoplasm / cytosol 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: 4.0 Å | |||||||||
![]() | Plaschka C / Lin P-C / Charenton C / Nagai K | |||||||||
![]() | ![]() タイトル: Prespliceosome structure provides insights into spliceosome assembly and regulation. 著者: Clemens Plaschka / Pei-Chun Lin / Clément Charenton / Kiyoshi Nagai / ![]() ![]() 要旨: The spliceosome catalyses the excision of introns from pre-mRNA in two steps, branching and exon ligation, and is assembled from five small nuclear ribonucleoprotein particles (snRNPs; U1, U2, U4, ...The spliceosome catalyses the excision of introns from pre-mRNA in two steps, branching and exon ligation, and is assembled from five small nuclear ribonucleoprotein particles (snRNPs; U1, U2, U4, U5, U6) and numerous non-snRNP factors. For branching, the intron 5' splice site and the branch point sequence are selected and brought by the U1 and U2 snRNPs into the prespliceosome, which is a focal point for regulation by alternative splicing factors. The U4/U6.U5 tri-snRNP subsequently joins the prespliceosome to form the complete pre-catalytic spliceosome. Recent studies have revealed the structural basis of the branching and exon-ligation reactions, however, the structural basis of the early events in spliceosome assembly remains poorly understood. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae prespliceosome at near-atomic resolution. The structure reveals an induced stabilization of the 5' splice site in the U1 snRNP, and provides structural insights into the functions of the human alternative splicing factors LUC7-like (yeast Luc7) and TIA-1 (yeast Nam8), both of which have been linked to human disease. In the prespliceosome, the U1 snRNP associates with the U2 snRNP through a stable contact with the U2 3' domain and a transient yeast-specific contact with the U2 SF3b-containing 5' region, leaving its tri-snRNP-binding interface fully exposed. The results suggest mechanisms for 5' splice site transfer to the U6 ACAGAGA region within the assembled spliceosome and for its subsequent conversion to the activation-competent B-complex spliceosome. Taken together, the data provide a working model to investigate the early steps of spliceosome assembly. | |||||||||
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 | ![]() | 627.1 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 48.3 KB 48.3 KB | 表示 表示 | ![]() |
画像 | ![]() | 34.8 KB | ||
その他 | ![]() | 613.8 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 250.5 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 249.6 KB | 表示 | |
XML形式データ | ![]() | 7.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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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 | Sharpened A2 map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.13 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
-追加マップ: Unsharpened A2 map
ファイル | emd_4364_additional.map | ||||||||||||
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注釈 | Unsharpened A2 map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : Prespliceosome A complex
+超分子 #1: Prespliceosome A complex
+分子 #1: U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA,U1 snRNA
+分子 #2: U2 snRNA
+分子 #11: Yeast UBC4 pre-mRNA (mutant)
+分子 #3: U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleop...
+分子 #4: U1 small nuclear ribonucleoprotein 70 kDa homolog,U1 small nuclea...
+分子 #5: U1 small nuclear ribonucleoprotein C
+分子 #6: Pre-mRNA-processing factor 39
+分子 #7: U1 small nuclear ribonucleoprotein component PRP42
+分子 #8: Protein NAM8
+分子 #9: 56 kDa U1 small nuclear ribonucleoprotein component
+分子 #10: Protein LUC7,Protein LUC7,Protein LUC7
+分子 #12: U1 small nuclear ribonucleoprotein component SNU71
+分子 #13: U2 snRNP component HSH155
+分子 #14: Pre-mRNA-splicing factor RSE1
+分子 #15: Cold sensitive U2 snRNA suppressor 1
+分子 #16: Protein HSH49
+分子 #17: Pre-mRNA-splicing factor RDS3
+分子 #18: Pre-mRNA-splicing factor PRP9
+分子 #19: Pre-mRNA-splicing factor PRP11,Pre-mRNA-splicing factor PRP11,Pre...
+分子 #20: Pre-mRNA-splicing factor PRP21
+分子 #21: U2 small nuclear ribonucleoprotein A'
+分子 #22: Unknown
+分子 #23: U2 small nuclear ribonucleoprotein B''
+分子 #24: RDS3 complex subunit 10
+分子 #25: Small nuclear ribonucleoprotein-associated protein B
+分子 #26: Small nuclear ribonucleoprotein Sm D3
+分子 #27: Small nuclear ribonucleoprotein E
+分子 #28: Small nuclear ribonucleoprotein F
+分子 #29: Small nuclear ribonucleoprotein G
+分子 #30: Small nuclear ribonucleoprotein Sm D1
+分子 #31: Small nuclear ribonucleoprotein Sm D2
+分子 #32: ZINC 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 | 0.4 mg/mL | |||||||||||||||||||||
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緩衝液 | pH: 7.9 構成要素:
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グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE | |||||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK III 詳細: Grids were blotted for 2-3.5 s and vitrified by plunging into liquid ethane with a FEI Vitrobot Mark III operated at 4 degree Celsius and 100% humidity.. |
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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 K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 実像数: 9407 / 平均電子線量: 43.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 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
精密化 | 空間: REAL |
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得られたモデル | ![]() PDB-6g90: |