5MQ0

Structure of a spliceosome remodeled for exon ligation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.17 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: 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 ...

    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.


    Related Citations: 
    • Structural basis of pre-mRNA splicing.
      Hang, J., Wan, R., Yan, C., Shi, Y.
      (2015) Science 349: 1191
    • The architecture of the spliceosomal U4/U6.U5 tri-snRNP.
      Nguyen, T.H., Galej, W.P., Bai, X.C., Savva, C.G., Newman, A.J., Scheres, S.H., Nagai, K.
      (2015) Nature 523: 47
    • Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 A resolution.
      Nguyen, T.H., Galej, W.P., Bai, X.C., Oubridge, C., Newman, A.J., Scheres, S.H., Nagai, K.
      (2016) Nature 530: 298
    • Cryo-EM structure of the spliceosome immediately after branching.
      Galej, W.P., Wilkinson, M.E., Fica, S.M., Oubridge, C., Newman, A.J., Nagai, K.
      (2016) Nature 537: 197

    Organizational Affiliation

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



Macromolecules

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8 A2413Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114 C1008Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 H577Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P53333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46 J451Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12417 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45 K379Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P28004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31 L157Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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Pre-mRNA-splicing factor CWC2 M339Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11 N364Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
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Pre-mRNA-splicing factor CEF1 O590Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
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Pre-mRNA-splicing factor CWC15 P175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
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Pre-mRNA-splicing factor CWC21 R135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CLF1 S687Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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Pre-mRNA-splicing factor SYF1,PRE-MRNA-SPLICING FACTOR SYF1 T877Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
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Pre-mRNA-splicing factor 18 a251Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
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Pre-mRNA-splicing factor SLU7 c382Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
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Pre-mRNA-processing factor 17 o455Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
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UNKNOWN PROTEIN X68Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
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Pre-mRNA-splicing factor SYF2 y215Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
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Small nuclear ribonucleoprotein-associated protein B bk196Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
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Small nuclear ribonucleoprotein Sm D3 dn101Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
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Small nuclear ribonucleoprotein E ep94Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
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Small nuclear ribonucleoprotein F fq86Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
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Small nuclear ribonucleoprotein G gr77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
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Small nuclear ribonucleoprotein Sm D1 hl146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
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Small nuclear ribonucleoprotein Sm D2 jm110Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
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Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22 V1145Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.13
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A' W238Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B'' Y111Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
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Pre-mRNA-splicing factor SNT309 s175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19 tuvw503Saccharomyces cerevisiaeMutation(s): 0 
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Yeast UBC4 gene for ubiquitin-conjugating enzymeI95Saccharomyces cerevisiae
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-EXON OF UBC4 PRE-MRNAE20Saccharomyces cerevisiae
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    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    S.cerevisiae chromosome II reading frame ORF YBR230c21175Saccharomyces cerevisiae
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    Entity ID: 4
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    Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence6112Saccharomyces cerevisiae
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    Entity ID: 5
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    Saccharomyces cerevisiae strain WI_C_MBSP_4 chromosome VII sequence5179Saccharomyces cerevisiae
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    • Entity ID: 34
      MoleculeChainsLengthOrganismImage
      3'-EXON OF UBC4 PRE-MRNA, BOUND BY PRP22 HELICASE33Saccharomyces cerevisiae
      Experimental Data & Validation

      Experimental Data

      • Method: ELECTRON MICROSCOPY
      • Resolution: 4.17 Å
      • Aggregation State: PARTICLE 
      • Reconstruction Method: SINGLE PARTICLE 

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Medical Research Council (United Kingdom)United KingdomMC_U105184330
      European Research Council693087
      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: 2018-10-24
        Changes: Advisory, Data collection, Derived calculations
      • Version 1.5: 2018-11-21
        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