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Yorodumi- PDB-8ro1: Structure of the C. elegans Intron Lariat Spliceosome double-prim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ro1 | ||||||
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Title | Structure of the C. elegans Intron Lariat Spliceosome double-primed for disassembly (ILS'') | ||||||
Components |
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Keywords | SPLICING / pre-mRNA splicing / intron lariat spliceosome / gene expression / spliceosome | ||||||
Function / homology | Function and homology information feminization of hermaphroditic germ-line / molting cycle / RNA lariat debranching enzyme activator activity / 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 ...feminization of hermaphroditic germ-line / molting cycle / RNA lariat debranching enzyme activator activity / 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 / 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 / rRNA processing / metallopeptidase activity / ubiquitin protein ligase activity / ribosome biogenesis / protein folding / regulation of gene expression / DNA replication / 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 Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Vorlaender, M.K. / Rothe, P. / Plaschka, C. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Nature / Year: 2024 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 8ro1.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8ro1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ro1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ro1_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8ro1_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8ro1_validation.xml.gz | 315.5 KB | Display | |
Data in CIF | 8ro1_validation.cif.gz | 522.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/8ro1 ftp://data.pdbj.org/pub/pdb/validation_reports/ro/8ro1 | HTTPS FTP |
-Related structure data
Related structure data | 19398MC 8ro0C 8ro2C 9fmdC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 4 types, 4 molecules 256IN
#1: RNA chain | Mass: 68422.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Full sequence: AUCGCUUCUUCGGCUUAUUAGCUAAGAUCAAAGUGUAGUAUCUGUUCUUAUCGUAUUAACCUACGGUAUACACUCGAAUGAGUGUAAUAAAGGUUAUAUGAUUUUUGGAACCUAGGGAAGACUCGGGGCUUGCUCCGACUUCCCAAGGGUCGUCCUGGCGUUGCACUGCUGCCGGGCUCGGCCCAGUCCCC Source: (natural) Caenorhabditis elegans (invertebrata) |
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#2: RNA chain | Mass: 35826.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) |
#3: RNA chain | Mass: 32483.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Caenorhabditis elegans (invertebrata) |
#10: RNA chain | Mass: 10348.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) |
-Pre-mRNA-splicing factor ... , 6 types, 6 molecules ADXIKMO
#4: Protein | Mass: 272396.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P34369 |
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#7: Protein | Mass: 84495.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q20875, RNA helicase |
#9: Protein | Mass: 99675.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P91175 |
#12: Protein | Mass: 27679.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q22417 |
#16: Protein | Mass: 27719.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q09385 |
#18: Protein | Mass: 45902.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q22412 |
-Protein , 16 types, 20 molecules CDJLNPPXQRTFXZbiopqrst
#5: Protein | Mass: 110612.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q23463 | ||||||
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#6: Protein | Mass: 31326.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q20716 | ||||||
#11: Protein | Mass: 88116.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O16376 | ||||||
#13: Protein | Mass: 85843.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: G5EFC4 | ||||||
#17: Protein | Mass: 17153.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P34313 | ||||||
#19: Protein | Mass: 26154.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O45766 | ||||||
#20: Protein | Mass: 94244.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: G5ECH1 | ||||||
#21: Protein | Mass: 170397.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9U1Q7 | ||||||
#22: Protein | Mass: 60303.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q22836 | ||||||
#25: Protein | Mass: 94421.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q17784 | ||||||
#27: Protein | Mass: 57466.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: G5EC45 | ||||||
#28: Protein | Mass: 8135.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q95XJ1 | ||||||
#30: Protein | Mass: 16768.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P91918 #36: Protein | | Mass: 28905.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9BLB6 #37: Protein | | Mass: 24881.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q21323 #38: Protein | Mass: 53272.633 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) References: UniProt: Q10051, RING-type E3 ubiquitin transferase |
-WD REPEATS REGION domain-containing ... , 3 types, 3 molecules ETW
#8: Protein | Mass: 36865.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q19211 |
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#24: Protein | Mass: 54766.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: G5EEL2 |
#26: Protein | Mass: 65385.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O44729 |
-CWF19-like protein ... , 2 types, 2 molecules L1L2
#14: Protein | Mass: 59034.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O16216 |
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#15: Protein | Mass: 53269.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q10946 |
-Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules Sy
#23: Protein | Mass: 18547.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q18445, peptidylprolyl isomerase |
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#39: Protein | Mass: 8825.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9U2S6, peptidylprolyl isomerase |
-Small nuclear ribonucleoprotein Sm ... , 2 types, 4 molecules ahcj
#29: Protein | Mass: 14836.212 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q17348 #31: Protein | Mass: 13724.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: E3LR34 |
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-Probable small nuclear ribonucleoprotein ... , 4 types, 8 molecules dkelfmgn
#32: Protein | Mass: 13291.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: MSAQAKPRSEMTAEELAAKEDEEFNVGPLSILTNSVKNNHQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKKAKSVAKDRFISKMFLRGDSVILVVKNPLAQAE Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q18786 #33: Protein | Mass: 10625.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9XTU6 #34: Protein | Mass: 9256.534 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P34659 #35: Protein | Mass: 8756.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9N4G9 |
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-Non-polymers , 4 types, 17 molecules
#40: Chemical | ChemComp-MG / #41: Chemical | #42: Chemical | ChemComp-GTP / | #43: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Intron lariat spliceosome (ILS'') / Type: COMPLEX / Entity ID: #1-#39 / Source: NATURAL |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 750 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 247908 / Symmetry type: POINT |