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: https://doi.org/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 Prp8F [auth A]2,413Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C
UniProt
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114G [auth B]1,008Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU114, GIN10, YKL173W, YKL637
UniProt
Find proteins for P36048 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46H [auth D]451Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP46, CWC1, NTC50, YPL151C, P2594
UniProt
Find proteins for Q12417 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45I [auth E]379Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP45, FUN20, YAL032C
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Entity ID: 10
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Pre-mRNA-splicing factor SLT11J [auth F]364Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM2, SLT11, YBR065C, YBR0614
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2K [auth G]339Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC2, NTC40, SLC3, YDL209C, D1041
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15L [auth H]175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC15, YDR163W, YD8358.17
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Entity ID: 13
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Pre-mRNA-splicing factor BUD31M [auth I]157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD31, CWC14, YCR063W, YCR63W, YCR903
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Entity ID: 14
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Pre-mRNA-splicing factor CWC21N [auth K]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC21, YDR482C
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22O [auth L]577Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CWC22, YGR278W
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor Prp17P [auth M]455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC40, PRP17, SLU4, XRS2, YDR364C, D9481.11
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Entity ID: 17
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Pre-mRNA-splicing factor Prp18Q [auth N]251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP18, YGR006W
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Entity ID: 18
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Pre-mRNA-splicing factor SLU7R [auth O]382Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SLU7, SLT17, YDR088C, D4483
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Entity ID: 19
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Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22S [auth P]1,145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP22, YER013W
EC: 3.6.4.13
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Entity ID: 20
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Pre-mRNA-splicing factor SYF2T [auth R]215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF2, NTC31, YGR129W
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Entity ID: 21
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Pre-mRNA-splicing factor CEF1U [auth S]590Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CEF1, NTC85, YMR213W, YM8261.07
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Entity ID: 22
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Pre-mRNA-splicing factor CLF1V [auth T]687Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CLF1, NTC77, SYF3, YLR117C, L2952
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Entity ID: 23
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Pre-mRNA-splicing factor SYF1W [auth U]859Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SYF1, NTC90, YDR416W
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown protein fragment219Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
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Unknown protein fragment16Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2MA [auth q],
Z [auth a]		110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2, YLR275W, L9328.5
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FAA [auth b],
IA [auth m]		86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3, YPR182W, P9705.4
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Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EBA [auth c],
HA [auth l]		94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1, YOR159C
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Entity ID: 29
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Small nuclear ribonucleoprotein GCA [auth d],
JA [auth n]		77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2, SNP2, YFL017W-A, YFL017Bw
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Entity ID: 30
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Small nuclear ribonucleoprotein-associated protein BDA [auth f],
GA [auth k]		196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1, YER029C
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Entity ID: 31
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Small nuclear ribonucleoprotein Sm D3EA [auth g],
KA [auth o]		101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3, YLR147C, L9634.6
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1FA [auth h],
LA [auth p]		146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1, YGR074W
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Entity ID: 33
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Lea1NA [auth r]111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSL1, YIR009W, YIB9W
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Entity ID: 34
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Msl1OA [auth s]238Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LEA1, YPL213W
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor Prp19PA [auth u],
QA [auth v],
RA [auth w],
SA [auth x]		503Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP19, PSO4, YLL036C
EC: 2.3.2.27
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Entity ID: 36
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Pre-mRNA-splicing factor SNT309TA [auth y]175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNT309, NTC25, YPR101W
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U2 snRNAA [auth 2]1,175Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U5 snRNAB [auth 5]214Saccharomyces cerevisiae
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Entity ID: 3
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U6 snRNAC [auth 6]112Saccharomyces cerevisiae
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Entity ID: 4
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RNA (34-MER)D [auth e]34Saccharomyces cerevisiae
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Entity ID: 5
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RNA (59-MER)E [auth i]59Saccharomyces cerevisiae
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP
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YA [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N		 Ligand Interaction
GTP
Query on GTP
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ZA [auth B]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
ZN
Query on ZN
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BB [auth F]
CB [auth F]
DB [auth G]
EB [auth I]
FB [auth I]
BB [auth F],
CB [auth F],
DB [auth G],
EB [auth I],
FB [auth I],
GB [auth I],
HB [auth O]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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AB [auth B],
UA [auth 6],
VA [auth 6],
WA [auth 6],
XA [auth 6]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1

Structure Validation

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View more in-depth experimental data
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