8RO1

Structure of the C. elegans Intron Lariat Spliceosome double-primed for disassembly (ILS'')


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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, 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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8 homologD [auth A]2,329Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tr-type G domain-containing proteinE [auth C]974Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q23463 (Caenorhabditis elegans)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Protein isy-1F [auth D]267Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase ddx-15G [auth DX]739Caenorhabditis elegansMutation(s): 0 
EC: 3.6.4.13
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
WD_REPEATS_REGION domain-containing proteinH [auth E]331Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q19211 (Caenorhabditis elegans)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1855Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
TPR_REGION domain-containing proteinK [auth J]744Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27L [auth K]238Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinM [auth L]755Caenorhabditis elegansMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
CWF19-like protein 1 homologN [auth L1]533Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
CWF19-like protein 2 homologO [auth L2]460Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor syf-2P [auth M]234Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homologQ [auth N]147Caenorhabditis elegansMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22R [auth O]408Caenorhabditis elegansMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologS [auth P]230Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
GCF C-terminal domain-containing proteinT [auth PX]809Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-binding protein aquariusU [auth Q]1,467Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein T27F2.1V [auth R]535Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseW [auth S]169Caenorhabditis elegansMutation(s): 0 
EC: 5.2.1.8
UniProt
Find proteins for Q18445 (Caenorhabditis elegans)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
WD_REPEATS_REGION domain-containing proteinX [auth T]494Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for G5EEL2 (Caenorhabditis elegans)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Septin and tuftelin-interacting protein 1 homologY [auth TF]830Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q17784 (Caenorhabditis elegans)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
WD_REPEATS_REGION domain-containing proteinZ [auth W]567Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O44729 (Caenorhabditis elegans)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Replication stress response regulator SDE2AA [auth X]500Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 12BA [auth Z]69Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q95XJ1 (Caenorhabditis elegans)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3CA [auth a],
JA [auth h]
136Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q17348 (Caenorhabditis elegans)
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UniProt GroupQ17348
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Probable small nuclear ribonucleoprotein-associated protein BDA [auth b],
KA [auth i]
160Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1EA [auth c],
LA [auth j]
127Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Probable small nuclear ribonucleoprotein Sm D2FA [auth d],
MA [auth k]
118Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Probable small nuclear ribonucleoprotein EGA [auth e],
NA [auth l]
90Caenorhabditis elegansMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Probable small nuclear ribonucleoprotein FHA [auth f],
OA [auth m]
85Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Probable small nuclear ribonucleoprotein GIA [auth g],
PA [auth n]
77Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Probable U2 small nuclear ribonucleoprotein A'QA [auth o]253Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
RRM domain-containing proteinRA [auth p]217Caenorhabditis elegansMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19SA [auth q],
TA [auth r],
UA [auth s],
VA [auth t]
492Caenorhabditis elegansMutation(s): 0 
EC: 2.3.2.27
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EWA [auth y]79Caenorhabditis elegansMutation(s): 0 
EC: 5.2.1.8
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
U2 snRNAA [auth 2]228Caenorhabditis elegans
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Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNAB [auth 5]112Caenorhabditis elegans
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Entity ID: 3
MoleculeChains LengthOrganismImage
U6 snRNAC [auth 6]101Caenorhabditis elegans
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Entity ID: 10
MoleculeChains LengthOrganismImage
Intron lariat RNAJ [auth IN]51Caenorhabditis elegans
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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DB [auth A],
GB [auth J]
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
Query on GTP

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EB [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN

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HB [auth L2]
IB [auth N]
JB [auth N]
KB [auth N]
LB [auth O]
HB [auth L2],
IB [auth N],
JB [auth N],
KB [auth N],
LB [auth O],
MB [auth O],
NB [auth O]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth 6]
BB [auth 6]
CB [auth 6]
FB [auth C]
XA [auth 6]
AB [auth 6],
BB [auth 6],
CB [auth 6],
FB [auth C],
XA [auth 6],
YA [auth 6],
ZA [auth 6]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Data collection, Database references