+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0360 | |||||||||||||||
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タイトル | Saccharomyces cerevisiae spliceosomal E complex (UBC4) | |||||||||||||||
マップデータ | Spliceosomal E complex (UBC4) | |||||||||||||||
試料 |
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キーワード | pre-mRNA splicing / spliceosome (スプライセオソーム) / E complex / RNA BINDING PROTEIN (RNA結合タンパク質) | |||||||||||||||
機能・相同性 | 機能・相同性情報 : / : / Processing of Intronless Pre-mRNAs / nuclear cap binding complex / positive regulation of RNA binding / RNA cap binding / primary miRNA processing / : / splicing factor binding / mRNA splice site recognition ...: / : / Processing of Intronless Pre-mRNAs / nuclear cap binding complex / positive regulation of RNA binding / RNA cap binding / primary miRNA processing / : / splicing factor binding / mRNA splice site recognition / U4/U6 snRNP / : / 7-methylguanosine cap hypermethylation / mRNA 3'-end processing / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / U2-type prespliceosome assembly / commitment complex / U4 snRNP / U2 snRNP / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process / U1 snRNP / U2-type prespliceosome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / pre-mRNA 5'-splice site binding / response to osmotic stress / precatalytic spliceosome / Processing of Capped Intron-Containing Pre-mRNA / Formation of the Early Elongation Complex / mRNA Capping / spliceosomal complex assembly / RNA Polymerase II Pre-transcription Events / 7-methylguanosine mRNA capping / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA 5'-splice site recognition / mRNA transport / U5 snRNP / spliceosomal snRNP assembly / mRNA export from nucleus / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / mRNA binding / perinuclear region of cytoplasm / RNA binding / zinc ion binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) / Saccharomyces cerevisiae S288C (パン酵母) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å | |||||||||||||||
データ登録者 | Liu S / Li X | |||||||||||||||
資金援助 | 米国, 4件
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引用 | ジャーナル: Nature / 年: 2019 タイトル: A unified mechanism for intron and exon definition and back-splicing. 著者: Xueni Li / Shiheng Liu / Lingdi Zhang / Aaron Issaian / Ryan C Hill / Sara Espinosa / Shasha Shi / Yanxiang Cui / Kalli Kappel / Rhiju Das / Kirk C Hansen / Z Hong Zhou / Rui Zhao / 要旨: The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E ...The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E complex assembled on introns, providing a view of the earliest event in the splicing cycle that commits pre-mRNAs to splicing. The E complex architecture suggests that the same spliceosome can assemble across an exon, and that it either remodels to span an intron for canonical linear splicing (typically on short exons) or catalyses back-splicing to generate circular RNA (on long exons). The model is supported by our experiments, which show that an E complex assembled on the middle exon of yeast EFM5 or HMRA1 can be chased into circular RNA when the exon is sufficiently long. This simple model unifies intron definition, exon definition, and back-splicing through the same spliceosome in all eukaryotes and should inspire experiments in many other systems to understand the mechanism and regulation of these processes. | |||||||||||||||
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_0360.map.gz | 199.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0360-v30.xml emd-0360.xml | 37.2 KB 37.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_0360_fsc.xml | 13.6 KB | 表示 | FSCデータファイル |
画像 | emd_0360.png | 46.3 KB | ||
Filedesc metadata | emd-0360.cif.gz | 10.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0360 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0360 | HTTPS FTP |
-関連構造データ
-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_0360.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Spliceosomal E complex (UBC4) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.36 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
-試料の構成要素
+全体 : Saccharomyces cerevisiae spliceosomal E complex (EBC4)
+超分子 #1: Saccharomyces cerevisiae spliceosomal E complex (EBC4)
+分子 #1: U1 small nuclear ribonucleoprotein 70 kDa homolog
+分子 #2: U1 small nuclear ribonucleoprotein C
+分子 #3: U1 small nuclear ribonucleoprotein A
+分子 #4: U1 small nuclear ribonucleoprotein component PRP42
+分子 #5: Pre-mRNA-processing factor 39
+分子 #6: Protein NAM8
+分子 #7: 56 kDa U1 small nuclear ribonucleoprotein component
+分子 #8: U1 small nuclear ribonucleoprotein component SNU71,U1 small nucle...
+分子 #9: Protein LUC7
+分子 #10: Pre-mRNA-processing protein PRP40
+分子 #11: Small nuclear ribonucleoprotein-associated protein B
+分子 #12: Small nuclear ribonucleoprotein Sm D1
+分子 #13: Small nuclear ribonucleoprotein Sm D2
+分子 #14: Small nuclear ribonucleoprotein Sm D3
+分子 #15: Small nuclear ribonucleoprotein E
+分子 #16: Small nuclear ribonucleoprotein F
+分子 #17: Small nuclear ribonucleoprotein G
+分子 #20: Nuclear cap-binding protein complex subunit 1
+分子 #21: Nuclear cap-binding protein subunit 2
+分子 #18: U1 snRNA
+分子 #19: UBC4 pre-mRNA
+分子 #22: 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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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: 7.9 |
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グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy |
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 / 平均電子線量: 30.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |