+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-19397 | |||||||||
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タイトル | Composite map of the C. elegans Intron Lariat Spliceosome primed for disassembly (ILS') | |||||||||
マップデータ | Composite Map | |||||||||
試料 |
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キーワード | mRNA / splicing / Intorn Lariat spliceosome / ILS / pre-mRNA | |||||||||
機能・相同性 | 機能・相同性情報 feminization of hermaphroditic germ-line / molting cycle / regulation of primary miRNA processing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / mRNA Splicing - Minor Pathway / germline cell cycle switching, mitotic to meiotic cell cycle / Formation of TC-NER Pre-Incision Complex ...feminization of hermaphroditic germ-line / molting cycle / regulation of primary miRNA processing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / mRNA Splicing - Minor Pathway / germline cell cycle switching, mitotic to meiotic cell cycle / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / vulval development / nematode larval development / egg-laying behavior / post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / spliceosomal complex disassembly / post-mRNA release spliceosomal complex / apoptotic DNA fragmentation / nuclear mRNA surveillance / generation of catalytic spliceosome for first transesterification step / nuclease activity / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U12-type spliceosomal complex / Prp19 complex / snRNP binding / locomotion / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / commitment complex / U2-type catalytic step 2 spliceosome / embryo development ending in birth or egg hatching / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / cyclosporin A binding / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / germ cell development / uterus development / protein K63-linked ubiquitination / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / helicase activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / mRNA processing / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / protein folding / regulation of gene expression / nucleic acid binding / RNA helicase activity / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA helicase / cell division / intracellular membrane-bounded organelle / DNA repair / GTPase activity / mRNA binding / GTP binding / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding 類似検索 - 分子機能 | |||||||||
生物種 | Caenorhabditis elegans (センチュウ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.9 Å | |||||||||
データ登録者 | Vorlaender MK / Rothe P / Plaschka C | |||||||||
資金援助 | European Union, 1件
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引用 | ジャーナル: Nature / 年: 2024 タイトル: Mechanism for the initiation of spliceosome disassembly. 著者: Matthias K Vorländer / Patricia Rothe / Justus Kleifeld / Eric D Cormack / Lalitha Veleti / Daria Riabov-Bassat / Laura Fin / Alex W Phillips / Luisa Cochella / Clemens Plaschka / 要旨: Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome. Recent studies have shed light on ...Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome. Recent studies have shed light on spliceosome assembly and remodelling for catalysis, but the mechanism of disassembly remains unclear. Here we report cryo-electron microscopy structures of nematode and human terminal intron lariat spliceosomes along with biochemical and genetic data. Our results uncover how four disassembly factors and the conserved RNA helicase DHX15 initiate spliceosome disassembly. The disassembly factors probe large inner and outer spliceosome surfaces to detect the release of ligated mRNA. Two of these factors, TFIP11 and C19L1, and three general spliceosome subunits, SYF1, SYF2 and SDE2, then dock and activate DHX15 on the catalytic U6 snRNA to initiate disassembly. U6 therefore controls both the start and end of pre-mRNA splicing. Taken together, our results explain the molecular basis of the initiation of canonical spliceosome disassembly and provide a framework to understand general spliceosomal RNA helicase control and the discard of aberrant spliceosomes. | |||||||||
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_19397.map.gz | 8.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-19397-v30.xml emd-19397.xml | 60.8 KB 60.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_19397.png | 136.7 KB | ||
Filedesc metadata | emd-19397.cif.gz | 18.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-19397 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19397 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_19397_validation.pdf.gz | 374.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_19397_full_validation.pdf.gz | 373.7 KB | 表示 | |
XML形式データ | emd_19397_validation.xml.gz | 7.3 KB | 表示 | |
CIF形式データ | emd_19397_validation.cif.gz | 8.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19397 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19397 | HTTPS FTP |
-関連構造データ
関連構造データ | 8ro0MC 8ro1C 8ro2C 9fmdC 50558 C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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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_19397.map.gz / 形式: CCP4 / 大きさ: 343 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Composite Map | ||||||||||||||||||||||||||||||||||||
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: 1.3013 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
-試料の構成要素
+全体 : Intron lariat spliceosome
+超分子 #1: Intron lariat spliceosome
+分子 #1: U2 snRNA
+分子 #2: U5 snRNA
+分子 #3: U6 snRNA
+分子 #4: Pre-mRNA-splicing factor 8 homolog
+分子 #5: U5 small nuclear ribonucleoprotein 200 kDa helicase
+分子 #6: Tr-type G domain-containing protein
+分子 #7: Protein isy-1
+分子 #8: WD_REPEATS_REGION domain-containing protein
+分子 #9: Pre-mRNA-splicing factor SYF1
+分子 #10: TPR_REGION domain-containing protein
+分子 #11: Pre-mRNA-splicing factor SPF27
+分子 #12: Cell division cycle 5-like protein
+分子 #13: Pre-mRNA-splicing factor syf-2
+分子 #14: Protein BUD31 homolog
+分子 #15: Pre-mRNA-splicing factor RBM22
+分子 #16: Spliceosome-associated protein CWC15 homolog
+分子 #17: GCF C-terminal domain-containing protein
+分子 #18: Intron-binding protein aquarius
+分子 #19: Uncharacterized protein T27F2.1
+分子 #20: Peptidyl-prolyl cis-trans isomerase
+分子 #21: WD_REPEATS_REGION domain-containing protein
+分子 #22: Septin and tuftelin-interacting protein 1 homolog
+分子 #23: WD_REPEATS_REGION domain-containing protein
+分子 #24: Coiled-coil domain-containing protein 12
+分子 #25: Small nuclear ribonucleoprotein Sm D3
+分子 #26: Probable small nuclear ribonucleoprotein-associated protein B
+分子 #27: Small nuclear ribonucleoprotein Sm D1
+分子 #28: Probable small nuclear ribonucleoprotein Sm D2
+分子 #29: Probable small nuclear ribonucleoprotein E
+分子 #30: Probable small nuclear ribonucleoprotein F
+分子 #31: Probable small nuclear ribonucleoprotein G
+分子 #32: Probable U2 small nuclear ribonucleoprotein A'
+分子 #33: RRM domain-containing protein
+分子 #34: Pre-mRNA-processing factor 19
+分子 #35: Peptidyl-prolyl cis-trans isomerase E
+分子 #36: Intron lariat RNA
+分子 #37: MAGNESIUM ION
+分子 #38: INOSITOL HEXAKISPHOSPHATE
+分子 #39: GUANOSINE-5'-TRIPHOSPHATE
+分子 #40: 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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凍結 | 凍結剤: ETHANE |
詳細 | Crosslinked with glutaraledhyde |
-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 BIOQUANTUM (6k x 4k) 平均電子線量: 60.0 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 / 最大 デフォーカス(公称値): 2.0 µm 最小 デフォーカス(公称値): 0.7000000000000001 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-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: 2.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 879523 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
-原子モデル構築 1
初期モデル | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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精密化 | プロトコル: AB INITIO MODEL |
得られたモデル | PDB-8ro0: |