+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 / E complex / RNA BINDING PROTEIN | |||||||||||||||
機能・相同性 | 機能・相同性情報 : / : / Processing of Intronless Pre-mRNAs / nuclear cap binding complex / RNA cap binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / primary miRNA processing / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP ...: / : / Processing of Intronless Pre-mRNAs / nuclear cap binding complex / RNA cap binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / primary miRNA processing / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / mRNA 3'-end processing / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / mRNA cis splicing, via spliceosome / commitment complex / poly(U) RNA binding / U2-type prespliceosome assembly / U4 snRNP / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / U1 snRNP / response to osmotic stress / pre-mRNA 5'-splice site binding / U2-type prespliceosome / Processing of Capped Intron-Containing Pre-mRNA / nuclear-transcribed mRNA catabolic process / Formation of the Early Elongation Complex / mRNA Capping / RNA Polymerase II Pre-transcription Events / precatalytic spliceosome / spliceosomal complex assembly / 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 / 7-methylguanosine mRNA capping / mRNA transport / U5 snRNP / mRNA export from nucleus / spliceosomal snRNP assembly / 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 / nucleus / cytoplasm / cytosol 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 |
-検証レポート
文書・要旨 | emd_0360_validation.pdf.gz | 594.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0360_full_validation.pdf.gz | 593.9 KB | 表示 | |
XML形式データ | emd_0360_validation.xml.gz | 13.5 KB | 表示 | |
CIF形式データ | emd_0360_validation.cif.gz | 18.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0360 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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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 |
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 |