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- PDB-8ro1: Structure of the C. elegans Intron Lariat Spliceosome double-prim... -
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Open data
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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'') | ||||||
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![]() | SPLICING / pre-mRNA splicing / intron lariat spliceosome / gene expression / spliceosome | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
![]() | Vorlaender, M.K. / Rothe, P. / Plaschka, C. | ||||||
Funding support | European Union, 1items
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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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 2.9 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 315.5 KB | Display | |
Data in CIF | ![]() | 522.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 19398MC ![]() 8ro0C ![]() 9fmdC ![]() 8ro2 C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() |
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#2: RNA chain | Mass: 35826.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: RNA chain | Mass: 32483.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#10: RNA chain | Mass: 10348.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() |
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#7: Protein | Mass: 84495.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 99675.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 27679.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 27719.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 45902.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() | ||||||
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#6: Protein | Mass: 31326.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#11: Protein | Mass: 88116.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#13: Protein | Mass: 85843.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#17: Protein | Mass: 17153.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#19: Protein | Mass: 26154.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#20: Protein | Mass: 94244.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#21: Protein | Mass: 170397.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#22: Protein | Mass: 60303.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#25: Protein | Mass: 94421.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#27: Protein | Mass: 57466.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#28: Protein | Mass: 8135.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#30: Protein | Mass: 16768.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #36: Protein | | Mass: 28905.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #37: Protein | | Mass: 24881.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #38: Protein | Mass: 53272.633 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() 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) ![]() ![]() |
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#24: Protein | Mass: 54766.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#26: Protein | Mass: 65385.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() |
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#15: Protein | Mass: 53269.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() |
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#39: Protein | Mass: 8825.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() #31: Protein | Mass: 13724.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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) ![]() ![]() #33: Protein | Mass: 10625.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #34: Protein | Mass: 9256.534 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #35: Protein | Mass: 8756.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 4 types, 17 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/IHP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/IHP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/ZN.gif)
#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 |
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Sample preparation
Component | Name: Intron lariat spliceosome (ILS'') / Type: COMPLEX / Entity ID: #1-#39 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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) |
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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 |