8RO2

Integrative Structure of the human intron lariat Spliceosome (ILS'')


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Mechanism for the initiation of spliceosome disassembly.

Vorlander, M.K.Rothe, P.Kleifeld, J.Cormack, E.D.Veleti, L.Riabov-Bassat, D.Fin, L.Phillips, A.W.Cochella, L.Plaschka, C.

(2024) Nature 632: 443-450

  • DOI: https://doi.org/10.1038/s41586-024-07741-1
  • Primary Citation of Related Structures:  
    8RO0, 8RO1, 8RO2, 9FMD

  • PubMed Abstract: 

    Pre-mRNA splicing requires the assembly, remodeling, and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome 1 . Recent studies have shed light on spliceosome assembly and remodeling for catalysis 2-6 , but the mechanism of disassembly remains unclear. Here, we report 2.6 to 3.2 Å resolution 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 thus controls both the start 5 and end of pre-mRNA splicing. Taken together, our results explain the molecular basis of canonical spliceosome disassembly and provide a framework to understand general spliceosomal RNA helicase control and the discard of aberrant spliceosomes.


  • Organizational Affiliation

    Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein component972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1 homolog285Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000240682 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DHX15E [auth DX]795Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000109606 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinF [auth E]357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1G [auth J]848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27H [auth K]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116752 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
CWF19-like protein 1I [auth L1]538Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000095485 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homologJ [auth N]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106245 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22K [auth O]420Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086589 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-binding protein aquariusL [auth Q]1,485Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000021776 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1M [auth R]536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1N [auth S]166Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000137168 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17O [auth W]579Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168438 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 12P [auth Z]166Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000160799 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3Q [auth a]126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1R [auth c]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2S [auth d]118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein ET [auth e]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FU [auth f]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GV [auth g]76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19LA [auth q],
MA [auth r],
NA [auth t],
W [auth s]
504Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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GTEx:  ENSG00000110107 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing regulator SDE2X [auth z]451Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143751 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor ESS-2 homologY [auth 3]476Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100056 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8AA [auth A]2,335Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174231 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1BA [auth I]855Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000076924 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinDA [auth L]802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
CWF19-like protein 2EA [auth L2]894Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000152404 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2FA [auth M]243Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117614 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologGA [auth P]229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
PAX3- and PAX7-binding protein 1HA [auth PX]917Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159086 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1IA [auth T]514Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Tuftelin-interacting protein 11JA [auth TF]837Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100109 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'KA [auth b]240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 1
MoleculeChains LengthOrganismImage
U2 snRNAA [auth 2]188Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
U6 snRNAB [auth 6]106Homo sapiens
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Entity ID: 26
MoleculeChains LengthOrganismImage
U5 snRNAZ [auth 5]116Homo sapiens
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Entity ID: 29
MoleculeChains LengthOrganismImage
INTRONCA [auth IN]154Homo sapiens
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release