6EXN

Post-catalytic P complex spliceosome with 3' splice site docked


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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

Postcatalytic spliceosome structure reveals mechanism of 3'-splice site selection.

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

(2017) Science 358: 1283-1288

  • DOI: 10.1126/science.aar3729
  • Primary Citation of Related Structures:  
    6EXN

  • PubMed Abstract: 
  • Introns are removed from eukaryotic messenger RNA precursors by the spliceosome in two transesterification reactions-branching and exon ligation. The mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3 ...

    Introns are removed from eukaryotic messenger RNA precursors by the spliceosome in two transesterification reactions-branching and exon ligation. The mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3.7-angstrom cryo-electron microscopy structure of the yeast P-complex spliceosome immediately after exon ligation. The 3'-splice site AG dinucleotide is recognized through non-Watson-Crick pairing with the 5' splice site and the branch-point adenosine. After the branching reaction, protein factors work together to remodel the spliceosome and stabilize a conformation competent for 3'-splice site docking, thereby promoting exon ligation. The structure accounts for the strict conservation of the GU and AG dinucleotides at the 5' and 3' ends of introns and provides insight into the catalytic mechanism of exon ligation.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. mwilkin@mrc-lmb.cam.ac.uk kn@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor Prp8 A2413Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8DBF3DNA39RNA8SLT21USA2YHR165C
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114 C1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114GIN10YKL173WYKL637
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC16 D278Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YJU2CWC16YKL095WYKL442
Find proteins for P28320 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 H577Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC22YGR278W
Find proteins for P53333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46 J451Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP46CWC1NTC50YPL151CP2594
Find proteins for Q12417 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45 K379Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP45FUN20YAL032C
Find proteins for P28004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31 L157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD31CWC14YCR063WYCR63WYCR903
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2 M339Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC2NTC40SLC3YDL209CD1041
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11 N364Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM2SLT11YBR065CYBR0614
Find proteins for P38241 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1 O590Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CEF1NTC85YMR213WYM8261.07
Find proteins for Q03654 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15 P175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC15YDR163WYD8358.17
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21 R135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC21YDR482C
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CLF1 S687Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CLF1NTC77SYF3YLR117CL2952
Find proteins for Q12309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1 T859Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF1NTC90YDR416W
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22 V1145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP22YER013W
EC: 3.6.4.13
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A' W238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LEA1YPL213W
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned structure X95Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B'' Y111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSL1YIR009WYIB9W
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor Prp18 a251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP18YGR006W
Find proteins for P33411 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein B bk196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1YER029C
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7 c382Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SLU7SLT17YDR088CD4483
Find proteins for Q02775 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3 dn101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3YLR147CL9634.6
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein E ep94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein F fq86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3YPR182WP9705.4
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein G gr77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1 hl146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1YGR074W
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2 jm110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor Prp17 o455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC40PRP17SLU4XRS2YDR364CD9481.11
Find proteins for P40968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNT309 s175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNT309NTC25YPR101W
Find proteins for Q06091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor Prp19 tuvw503Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP19PSO4YLL036C
EC: 2.3.2.27
Find proteins for P32523 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2 y215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF2NTC31YGR129W
Find proteins for P53277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U2 snRNA21175Saccharomyces cerevisiae S288C
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U5 snRNA5179Saccharomyces cerevisiae S288C
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Entity ID: 3
MoleculeChainsLengthOrganismImage
U6 snRNA6112Saccharomyces cerevisiae S288C
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Entity ID: 7
MoleculeChainsLengthOrganismImage
Ligated exons: UBC4 mRNAE39Saccharomyces cerevisiae S288C
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Entity ID: 9
MoleculeChainsLengthOrganismImage
Intron lariat: UBC4 RNAI95Saccharomyces cerevisiae S288C
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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 CouncilUnited KingdomSPLICE3D
Medical Research Council (United Kingdom)United KingdomMC_U105184330

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Structure summary
  • Version 1.2: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Other
  • Version 2.0: 2020-10-07
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary