6N7X

S. cerevisiae U1 snRNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history


Literature

CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing.

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

(2017) Nat Commun 8: 1035-1035

  • DOI: 10.1038/s41467-017-01241-9
  • Primary Citation of Related Structures:  
    6N7X

  • PubMed Abstract: 
  • U1 snRNP plays a critical role in 5'-splice site recognition and is a frequent target of alternative splicing factors. These factors transiently associate with human U1 snRNP and are not amenable for structural studies, while their Saccharomyces cerevisiae (yeast) homologs are stable components of U1 snRNP ...

    U1 snRNP plays a critical role in 5'-splice site recognition and is a frequent target of alternative splicing factors. These factors transiently associate with human U1 snRNP and are not amenable for structural studies, while their Saccharomyces cerevisiae (yeast) homologs are stable components of U1 snRNP. Here, we report the cryoEM structure of yeast U1 snRNP at 3.6 Å resolution with atomic models for ten core proteins, nearly all essential domains of its RNA, and five stably associated auxiliary proteins. The foot-shaped yeast U1 snRNP contains a core in the "ball-and-toes" region architecturally similar to the human U1 snRNP. All auxiliary proteins are in the "arch-and-heel" region and connected to the core through the Prp42/Prp39 paralogs. Our demonstration that homodimeric human PrpF39 directly interacts with U1C-CTD, mirroring yeast Prp42/Prp39, supports yeast U1 snRNP as a model for understanding how transiently associated auxiliary proteins recruit human U1 snRNP in alternative splicing.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USA. rui.zhao@ucdenver.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein 70 kDa homolog A300Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNP1YIL061C
Find proteins for Q00916 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein C B231Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YHC1YLR298CL8003.21
Find proteins for Q05900 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein A C298Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MUD1YBR119WYBR0915
Find proteins for P32605 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein component PRP42 D544Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP42MUD16SNU65YDR235WYD8419.02
Find proteins for Q03776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 39 E629Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP39YML046WYM9827.06
Find proteins for P39682 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Protein NAM8 F523Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NAM8MRE2YHR086W
Find proteins for Q00539 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
56 kDa U1 small nuclear ribonucleoprotein component G492Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU56MUD10YDR240C
Find proteins for Q03782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein component SNU71 H620Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU71YGR013W
Find proteins for P53207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein B K196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMB1YER029C
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1 L146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD1YGR074W
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2 M110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD2YLR275WL9328.5
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3 N101Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMD3YLR147CL9634.6
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein E O94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SME1YOR159C
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein F P86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX3YPR182WP9705.4
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein G Q77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMX2SNP2YFL017W-AYFL017Bw
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsLengthOrganismImage
U1 snRNAR568Saccharomyces cerevisiae S288C
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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 Human Genome Research Institute (NIH/NHGRI)United StatesGM114178
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM114178-02S2
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM071940
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesAI094386

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-25
    Changes: Database references