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- PDB-6n7x: S. cerevisiae U1 snRNP -

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Basic information

Entry
Database: PDB / ID: 6n7x
TitleS. cerevisiae U1 snRNP
Components
  • (Small nuclear ribonucleoprotein ...) x 6
  • (U1 small nuclear ribonucleoprotein ...) x 5
  • 56 kDa U1 small nuclear ribonucleoprotein component
  • Pre-mRNA-processing factor 39
  • Protein NAM8
  • Small nuclear ribonucleoprotein-associated protein B
  • U1 snRNA
KeywordsRNA BINDING PROTEIN/RNA / pre-mRNA splicing / U1 snRNP / alternative splicing / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


mRNA splice site recognition / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / snRNP binding / positive regulation of mRNA splicing, via spliceosome / small nuclear ribonucleoprotein complex / splicing factor binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex ...mRNA splice site recognition / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / snRNP binding / positive regulation of mRNA splicing, via spliceosome / small nuclear ribonucleoprotein complex / splicing factor binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex / commitment complex / U2-type prespliceosome assembly / U2 snRNP / U1 snRNP / U4 snRNP / poly(U) RNA binding / U2-type prespliceosome / pre-mRNA 5'-splice site binding / precatalytic spliceosome / mRNA 5'-splice site recognition / spliceosomal complex assembly / Prp19 complex / U5 snRNP / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / mRNA binding / RNA binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Snu56-like U1 small nuclear ribonucleoprotein component / Snu56-like U1 small nuclear ribonucleoprotein component / SNU71 RNA binding domain / SNU71 N-terminal / U1 small nuclear ribonucleoprotein C / PRP39 C-terminal HAT repeat / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / : / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / : ...Snu56-like U1 small nuclear ribonucleoprotein component / Snu56-like U1 small nuclear ribonucleoprotein component / SNU71 RNA binding domain / SNU71 N-terminal / U1 small nuclear ribonucleoprotein C / PRP39 C-terminal HAT repeat / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / : / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / : / U1-C, C2H2-type zinc finger / U1 zinc finger / PWI domain / PWI, domain in splicing factors / PRP39 N-terminal HAT repeat / : / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / SH3 type barrels. - #100 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / : / Sm domain profile. / LSM domain superfamily / RRM (RNA recognition motif) domain / Zinc finger C2H2 superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / SH3 type barrels. / Tetratricopeptide-like helical domain superfamily / Roll / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein A / Pre-mRNA-processing factor 39 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / U1 small nuclear ribonucleoprotein component SNU71 / Small nuclear ribonucleoprotein F ...RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein A / Pre-mRNA-processing factor 39 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / U1 small nuclear ribonucleoprotein component SNU71 / Small nuclear ribonucleoprotein F / Protein NAM8 / U1 small nuclear ribonucleoprotein 70 kDa homolog / Small nuclear ribonucleoprotein Sm D1 / U1 small nuclear ribonucleoprotein component PRP42 / 56 kDa U1 small nuclear ribonucleoprotein component / U1 small nuclear ribonucleoprotein C / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLi, X. / Liu, S. / Jiang, J. / Zhang, L. / Espinosa, S. / Hill, R.C. / Hansen, K.C. / Zhou, Z.H. / Zhao, R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM114178 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM114178-02S2 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM071940 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI094386 United States
CitationJournal: Nat Commun / Year: 2017
Title: CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing.
Authors: Xueni Li / Shiheng Liu / Jiansen Jiang / Lingdi Zhang / Sara Espinosa / Ryan C Hill / Kirk C Hansen / Z Hong Zhou / Rui Zhao /
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 ...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.
History
DepositionNov 28, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJul 24, 2019ID: 5UZ5
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Database references / Category: database_2
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: U1 small nuclear ribonucleoprotein 70 kDa homolog
B: U1 small nuclear ribonucleoprotein C
C: U1 small nuclear ribonucleoprotein A
D: U1 small nuclear ribonucleoprotein component PRP42
E: Pre-mRNA-processing factor 39
F: Protein NAM8
G: 56 kDa U1 small nuclear ribonucleoprotein component
H: U1 small nuclear ribonucleoprotein component SNU71
K: Small nuclear ribonucleoprotein-associated protein B
L: Small nuclear ribonucleoprotein Sm D1
M: Small nuclear ribonucleoprotein Sm D2
N: Small nuclear ribonucleoprotein Sm D3
O: Small nuclear ribonucleoprotein E
P: Small nuclear ribonucleoprotein F
Q: Small nuclear ribonucleoprotein G
R: U1 snRNA


Theoretical massNumber of molelcules
Total (without water)694,67816
Polymers694,67816
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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U1 small nuclear ribonucleoprotein ... , 5 types, 5 molecules ABCDH

#1: Protein U1 small nuclear ribonucleoprotein 70 kDa homolog / U1-70K / U1 small nuclear ribonucleoprotein SNP1 / U1 snRNP protein SNP1


Mass: 34506.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q00916
#2: Protein U1 small nuclear ribonucleoprotein C / U1C


Mass: 27106.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q05900
#3: Protein U1 small nuclear ribonucleoprotein A / U1A / Mutant U1 die protein 1


Mass: 34438.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32605
#4: Protein U1 small nuclear ribonucleoprotein component PRP42 / U1 snRNP protein PRP42 / 65 kDa snRNP protein / Pre-mRNA-processing factor 42


Mass: 65222.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03776
#8: Protein U1 small nuclear ribonucleoprotein component SNU71


Mass: 71484.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53207

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Protein , 4 types, 4 molecules EFGK

#5: Protein Pre-mRNA-processing factor 39


Mass: 74834.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39682
#6: Protein Protein NAM8


Mass: 57010.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q00539
#7: Protein 56 kDa U1 small nuclear ribonucleoprotein component


Mass: 56575.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03782
#9: Protein Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / SmB


Mass: 22426.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40018

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Small nuclear ribonucleoprotein ... , 6 types, 6 molecules LMNOPQ

#10: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1


Mass: 16296.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02260
#11: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 12876.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06217
#12: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 11240.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P43321
#13: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10385.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12330
#14: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9669.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P54999
#15: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8490.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40204

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RNA chain , 1 types, 1 molecules R

#16: RNA chain U1 snRNA


Mass: 182114.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: S. cerevisiae U1 snRNP / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 51.9 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: Leginon / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 352900 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å

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