5MPS

Structure of a spliceosome remodeled for exon ligation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure of a spliceosome remodelled for exon ligation.

Fica, S.M.Oubridge, C.Galej, W.P.Wilkinson, M.E.Bai, X.C.Newman, A.J.Nagai, K.

(2017) Nature 542: 377-380

  • DOI: https://doi.org/10.1038/nature21078
  • Primary Citation of Related Structures:  
    5MPS, 5MQ0

  • PubMed Abstract: 

    The spliceosome excises introns from pre-mRNAs in two sequential transesterifications-branching and exon ligation-catalysed at a single catalytic metal site in U6 small nuclear RNA (snRNA). Recently reported structures of the spliceosomal C complex with the cleaved 5' exon and lariat-3'-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5' splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site. Here we present, at 3.8 Å resolution, the cryo-electron microscopy structure of a Saccharomyces cerevisiae spliceosome stalled after Prp16-mediated remodelling but before exon ligation. While the U6 snRNA catalytic core remains firmly held in the active site cavity of Prp8 by proteins common to both steps, the branch helix has rotated by 75° compared to the C complex and is stabilized in a new position by Prp17, Cef1 and the reoriented Prp8 RNase H-like domain. This rotation of the branch helix removes the branch adenosine from the catalytic core, creates a space for 3' exon docking, and restructures the pairing of the 5' splice site with the U6 snRNA ACAGAGA region. Slu7 and Prp18, which promote exon ligation, bind together to the Prp8 RNase H-like domain. The ATPase Prp22, bound to Prp8 in place of Prp16, could interact with the 3' exon, suggesting a possible basis for mRNA release after exon ligation. Together with the structure of the C complex, our structure of the C* complex reveals the two major conformations of the spliceosome during the catalytic stages of splicing.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.


Macromolecules

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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8F [auth A]2,413Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114G [auth C]1,008Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22577Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46I [auth J]451Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45J [auth K]379Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31K [auth L]157Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2L [auth M]339Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11M [auth N]364Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1N [auth O]590Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15O [auth P]175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21P [auth R]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CLF1Q [auth S]687Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1R [auth T]877Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 18S [auth a]251Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7T [auth c]382Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17U [auth o]455Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
UnknownV [auth X]68Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2W [auth y]215Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BX [auth b]196Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3Y [auth d]101Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EZ [auth e]94Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FAA [auth f]86Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GBA [auth g]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1CA [auth h]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2DA [auth j]110Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
Yeast UBC4 gene for ubiquitin-conjugating enzymeA [auth I]95Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChains LengthOrganismImage
UBC4 gene exonB [auth E]20Saccharomyces cerevisiae
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Entity ID: 3
MoleculeChains LengthOrganismImage
U2 snRNAC [auth 2]1,175Saccharomyces cerevisiae
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Entity ID: 4
MoleculeChains LengthOrganismImage
Saccharomyces cerevisiae strain T.52_2H chromosome XII sequenceD [auth 6]112Saccharomyces cerevisiae
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Entity ID: 5
MoleculeChains LengthOrganismImage
U5 snRNAE [auth 5]179Saccharomyces cerevisiae
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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JA [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
Query on GTP

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

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LA [auth L]
MA [auth L]
NA [auth L]
OA [auth M]
PA [auth N]
LA [auth L],
MA [auth L],
NA [auth L],
OA [auth M],
PA [auth N],
QA [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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HA [auth 6],
IA [auth 6]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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EA [auth 6],
FA [auth 6],
GA [auth 6]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTREFMAC5.8

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC-U105184330
European Research CouncilAdG-693087-SPLICE3D
EMBO and Marie Sklodowska-Curie FellowshipRef. S.M.Fica

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2017-07-05
    Changes: Data collection
  • Version 1.3: 2017-08-30
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2018-10-17
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.6: 2019-12-11
    Changes: Other
  • Version 2.0: 2020-10-07
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary