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- EMDB-19398: Structure of the C. elegans Intron Lariat Spliceosome double-prim... -
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Open data
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Basic information
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Title | Structure of the C. elegans Intron Lariat Spliceosome double-primed for disassembly (ILS'') | |||||||||
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![]() | pre-mRNA splicing / intron lariat spliceosome / gene expression / spliceosome / splicing | |||||||||
Function / homology | ![]() RNA lariat debranching enzyme activator activity / feminization of hermaphroditic germ-line / molting cycle / regulation of primary miRNA processing / SLBP independent Processing of Histone Pre-mRNAs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of Mature mRNA derived from an Intron-Containing Transcript ...RNA lariat debranching enzyme activator activity / feminization of hermaphroditic germ-line / molting cycle / regulation of primary miRNA processing / SLBP independent Processing of Histone Pre-mRNAs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / Downregulation of SMAD2/3:SMAD4 transcriptional activity / mRNA Splicing - Minor Pathway / germline cell cycle switching, mitotic to meiotic cell cycle / mRNA Splicing - Major Pathway / 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 / U12-type spliceosomal complex / Prp19 complex / snRNP binding / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / locomotion / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / 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 / cyclosporin A binding / precatalytic spliceosome / 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 / peptidylprolyl isomerase / helicase activity / 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 / rRNA processing / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / protein folding / ribosome biogenesis / regulation of gene expression / DNA replication / nucleic acid binding / cell differentiation / RNA helicase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA helicase / cell division / intracellular membrane-bounded organelle / DNA repair / GTPase activity / mRNA binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / GTP binding / apoptotic process / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Vorlaender MK / Rothe P / Plaschka C | |||||||||
Funding support | European Union, 1 items
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![]() | ![]() Title: Mechanism for the initiation of spliceosome disassembly. Authors: Matthias K Vorländer / Patricia Rothe / Justus Kleifeld / Eric D Cormack / Lalitha Veleti / Daria Riabov-Bassat / Laura Fin / Alex W Phillips / Luisa Cochella / Clemens Plaschka / ![]() ![]() Abstract: 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. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 63.6 KB 63.6 KB | Display Display | ![]() |
Images | ![]() | 126.8 KB | ||
Filedesc metadata | ![]() | 18.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 495.2 KB | Display | ![]() |
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Full document | ![]() | 494.7 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 4.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ro1MC ![]() 8ro0C ![]() 9fmdC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.3013 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Intron lariat spliceosome (ILS'')
+Supramolecule #1: Intron lariat spliceosome (ILS'')
+Macromolecule #1: U2 snRNA
+Macromolecule #2: U5 snRNA
+Macromolecule #3: U6 snRNA
+Macromolecule #10: Intron lariat RNA
+Macromolecule #4: Pre-mRNA-splicing factor 8 homolog
+Macromolecule #5: Tr-type G domain-containing protein
+Macromolecule #6: Protein isy-1
+Macromolecule #7: Pre-mRNA-splicing factor ATP-dependent RNA helicase ddx-15
+Macromolecule #8: WD_REPEATS_REGION domain-containing protein
+Macromolecule #9: Pre-mRNA-splicing factor SYF1
+Macromolecule #11: TPR_REGION domain-containing protein
+Macromolecule #12: Pre-mRNA-splicing factor SPF27
+Macromolecule #13: Cell division cycle 5-like protein
+Macromolecule #14: CWF19-like protein 1 homolog
+Macromolecule #15: CWF19-like protein 2 homolog
+Macromolecule #16: Pre-mRNA-splicing factor syf-2
+Macromolecule #17: Protein BUD31 homolog
+Macromolecule #18: Pre-mRNA-splicing factor RBM22
+Macromolecule #19: Spliceosome-associated protein CWC15 homolog
+Macromolecule #20: GCF C-terminal domain-containing protein
+Macromolecule #21: Intron-binding protein aquarius
+Macromolecule #22: Uncharacterized protein T27F2.1
+Macromolecule #23: Peptidyl-prolyl cis-trans isomerase
+Macromolecule #24: WD_REPEATS_REGION domain-containing protein
+Macromolecule #25: Septin and tuftelin-interacting protein 1 homolog
+Macromolecule #26: WD_REPEATS_REGION domain-containing protein
+Macromolecule #27: Replication stress response regulator SDE2
+Macromolecule #28: Coiled-coil domain-containing protein 12
+Macromolecule #29: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #30: Probable small nuclear ribonucleoprotein-associated protein B
+Macromolecule #31: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #32: Probable small nuclear ribonucleoprotein Sm D2
+Macromolecule #33: Probable small nuclear ribonucleoprotein E
+Macromolecule #34: Probable small nuclear ribonucleoprotein F
+Macromolecule #35: Probable small nuclear ribonucleoprotein G
+Macromolecule #36: Probable U2 small nuclear ribonucleoprotein A'
+Macromolecule #37: RRM domain-containing protein
+Macromolecule #38: Pre-mRNA-processing factor 19
+Macromolecule #39: Peptidyl-prolyl cis-trans isomerase E
+Macromolecule #40: MAGNESIUM ION
+Macromolecule #41: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #42: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #43: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 247908 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |