5UZ5

S. cerevisiae U1 snRNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 cere ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein 70 kDa homolog
A
300Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SNP1
Find proteins for Q00916 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q00916
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein C
B
231Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: YHC1
Find proteins for Q05900 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05900
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein A,TAP tag
C
484Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: MUD1
Find proteins for P32605 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32605
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein component PRP42
D
544Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP42 (MUD16, SNU65)
Find proteins for Q03776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03776
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 39
E
629Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP39
Find proteins for P39682 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39682
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Protein NAM8
F
523Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: NAM8 (MRE2)
Find proteins for Q00539 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q00539
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
56 kDa U1 small nuclear ribonucleoprotein component
G
492Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SNU56 (MUD10)
Find proteins for Q03782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03782
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Protein LUC7
H
261Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LUC7 (EPE1, EXM2)
Find proteins for Q07508 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07508
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated protein B
K
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMB1
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40018
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
L
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMD1
Find proteins for Q02260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02260
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
M
110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMD2
Find proteins for Q06217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06217
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
N
101Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMD3
Find proteins for P43321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43321
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
O
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SME1
Find proteins for Q12330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12330
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
P
86Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMX3
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P54999
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
Q
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SMX2 (SNP2)
Find proteins for P40204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40204
Entity ID: 16
MoleculeChainsLengthOrganism
RNAR568Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM114178
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM114178-02S2
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM071940
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI094386

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Author supporting evidence
  • Version 1.2: 2018-02-07
    Type: Source and taxonomy