6BK8

S. cerevisiae spliceosomal post-catalytic P complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the yeast spliceosomal postcatalytic P complex.

Liu, S.Li, X.Zhang, L.Jiang, J.Hill, R.C.Cui, Y.Hansen, K.C.Zhou, Z.H.Zhao, R.

(2017) Science 358: 1278-1283

  • DOI: 10.1126/science.aar3462
  • Primary Citation of Related Structures:  
    6BK8

  • PubMed Abstract: 
  • The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, B act , C, C*, and intron lariat spliceosome complexes revealed mechanisms of 5'-splice site (ss) recognition, branching, and intron release, but lacked information on 3'-ss recognition, exon ligation, and exon release ...

    The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, B act , C, C*, and intron lariat spliceosome complexes revealed mechanisms of 5'-splice site (ss) recognition, branching, and intron release, but lacked information on 3'-ss recognition, exon ligation, and exon release. Here we report a cryo-electron microscopy structure of the postcatalytic P complex at 3.3-angstrom resolution, revealing that the 3' ss is mainly recognized through non-Watson-Crick base pairing with the 5' ss and branch point. Furthermore, one or more unidentified proteins become stably associated with the P complex, securing the 3' exon and potentially regulating activity of the helicase Prp22. Prp22 binds nucleotides 15 to 21 in the 3' exon, enabling it to pull the intron-exon or ligated exons in a 3' to 5' direction to achieve 3'-ss proofreading or exon release, respectively.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA. rui.zhao@ucdenver.edu hong.zhou@ucla.edu.



Macromolecules

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Entity ID: 6
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: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114 B1008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114GIN10YKL173WYKL637
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46 D451Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP46CWC1NTC50YPL151CP2594
Find proteins for Q12417 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45 E379Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP45FUN20YAL032C
Find proteins for P28004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11 F364Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM2SLT11YBR065CYBR0614
Find proteins for P38241 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2 G339Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC2NTC40SLC3YDL209CD1041
Find proteins for Q12046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15 H175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC15YDR163WYD8358.17
Find proteins for Q03772 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor BUD31 I157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD31CWC14YCR063WYCR63WYCR903
Find proteins for P25337 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21 K135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC21YDR482C
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 L577Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC22YGR278W
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor Prp17 M455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC40PRP17SLU4XRS2YDR364CD9481.11
Find proteins for P40968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor Prp18 N251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP18YGR006W
Find proteins for P33411 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7 O382Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SLU7SLT17YDR088CD4483
Find proteins for Q02775 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22 P1145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP22YER013W
EC: 3.6.4.13
Find proteins for P24384 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2 R215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF2NTC31YGR129W
Find proteins for P53277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CEF1 S590Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CEF1NTC85YMR213WYM8261.07
Find proteins for Q03654 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CLF1 T687Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CLF1NTC77SYF3YLR117CL2952
Find proteins for Q12309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1 U859Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF1NTC90YDR416W
Find proteins for Q04048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown protein fragment X219Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown protein fragment Y16Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2 aq110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein F bm86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3YPR182WP9705.4
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein E cl94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein G dn77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein B fk196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1YER029C
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3 go101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3YLR147CL9634.6
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1 hp146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1YGR074W
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Lea1 r111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSL1YIR009WYIB9W
Find proteins for P40567 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Msl1 s238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LEA1YPL213W
Find proteins for Q08963 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor Prp19 uvwx503Saccharomyces 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 SNT309 y175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNT309NTC25YPR101W
Find proteins for Q06091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U2 snRNA21175Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U5 snRNA5214Saccharomyces cerevisiae
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Entity ID: 3
MoleculeChainsLengthOrganismImage
U6 snRNA6112Saccharomyces cerevisiae
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Entity ID: 4
MoleculeChainsLengthOrganismImage
RNA (34-MER)e34Saccharomyces cerevisiae
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Entity ID: 5
MoleculeChainsLengthOrganismImage
RNA (59-MER)i59Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM114178
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM071940
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI094386

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Author supporting evidence, Database references, Structure summary
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2020-10-14
    Changes: Advisory, Derived calculations, Structure summary