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- EMDB-0361: Saccharomyces cerevisiae spliceosomal E complex (ACT1) -

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Basic information

Entry
Database: EMDB / ID: EMD-0361
TitleSaccharomyces cerevisiae spliceosomal E complex (ACT1)
Map data
SampleSaccharomyces cerevisiae spliceosomal E complex (ACT1)
  • (U1 small nuclear ribonucleoprotein ...) x 5
  • Pre-mRNA-processing factor 39
  • Protein NAM8
  • 56 kDa U1 small nuclear ribonucleoprotein component
  • Protein LUC7
  • Small nuclear ribonucleoprotein-associated protein B
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (nucleic-acidNucleic acid) x 2
  • ligand
Function / homology
Function and homology information


positive regulation of RNA binding / mRNA splice site selection / splicing factor binding / positive regulation of mRNA splicing, via spliceosome / pICln-Sm protein complex / U4 snRNP / mRNA 5'-splice site recognition / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / pre-mRNA 5'-splice site binding ...positive regulation of RNA binding / mRNA splice site selection / splicing factor binding / positive regulation of mRNA splicing, via spliceosome / pICln-Sm protein complex / U4 snRNP / mRNA 5'-splice site recognition / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / pre-mRNA 5'-splice site binding / commitment complex / U12-type spliceosomal complex / U2 snRNP / small nucleolar ribonucleoprotein complex / U5 snRNP / U2-type prespliceosome / spliceosomal snRNP assembly / P granule / U1 snRNP / U4/U6 x U5 tri-snRNP complex / U1 snRNA binding / poly(U) RNA binding / catalytic step 2 spliceosome / mRNA splicing, via spliceosome / mRNA binding / mitochondrion / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Tetratricopeptide-like helical domain superfamily / Small nuclear ribonucleoprotein G / Sm-like protein Lsm6/SmF / LSM domain superfamily / Luc7-related / Matrin/U1-C-like, C2H2-type zinc finger / HAT (Half-A-TPR) repeat / PWI domain / LSM domain, eukaryotic/archaea-type / Matrin/U1-C, C2H2-type zinc finger ...Tetratricopeptide-like helical domain superfamily / Small nuclear ribonucleoprotein G / Sm-like protein Lsm6/SmF / LSM domain superfamily / Luc7-related / Matrin/U1-C-like, C2H2-type zinc finger / HAT (Half-A-TPR) repeat / PWI domain / LSM domain, eukaryotic/archaea-type / Matrin/U1-C, C2H2-type zinc finger / RNA recognition motif domain / U1 small nuclear ribonucleoprotein C / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / Small nuclear ribonucleoprotein E / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / U1-C, C2H2-type zinc finger / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / U1 small nuclear ribonucleoprotein 70kDa / Zinc finger matrin-type profile. / Eukaryotic RNA Recognition Motif (RRM) profile. / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / U1 zinc finger / LUC7 N_terminus / LSM domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Nucleotide-binding alpha-beta plait domain superfamily / Zinc finger C2H2 superfamily / RNA-binding domain superfamily / snRNP70, RNA recognition motif / Small nuclear ribonucleoprotein F
U1 small nuclear ribonucleoprotein 70 kDa homolog / Protein LUC7 / Small nuclear ribonucleoprotein Sm D2 / U1 small nuclear ribonucleoprotein C / 56 kDa U1 small nuclear ribonucleoprotein component / U1 small nuclear ribonucleoprotein component PRP42 / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein F / Protein NAM8 / U1 small nuclear ribonucleoprotein component SNU71 ...U1 small nuclear ribonucleoprotein 70 kDa homolog / Protein LUC7 / Small nuclear ribonucleoprotein Sm D2 / U1 small nuclear ribonucleoprotein C / 56 kDa U1 small nuclear ribonucleoprotein component / U1 small nuclear ribonucleoprotein component PRP42 / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein F / Protein NAM8 / U1 small nuclear ribonucleoprotein component SNU71 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein-associated protein B / Pre-mRNA-processing factor 39 / U1 small nuclear ribonucleoprotein A / Small nuclear ribonucleoprotein E
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu S / Li X / Zhou ZH / Zhao R
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteGM126157 United States
National Institutes of Health/National Human Genome Research InstituteGM071940 United States
National Institutes of Health/National Human Genome Research InstituteGM114178 United States
National Institutes of Health/National Human Genome Research InstituteAI094386 United States
CitationJournal: Nature / Year: 2019
Title: A unified mechanism for intron and exon definition and back-splicing.
Authors: Xueni Li / Shiheng Liu / Lingdi Zhang / Aaron Issaian / Ryan C Hill / Sara Espinosa / Shasha Shi / Yanxiang Cui / Kalli Kappel / Rhiju Das / Kirk C Hansen / Z Hong Zhou / Rui Zhao /
Abstract: The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E ...The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E complex assembled on introns, providing a view of the earliest event in the splicing cycle that commits pre-mRNAs to splicing. The E complex architecture suggests that the same spliceosome can assemble across an exon, and that it either remodels to span an intron for canonical linear splicing (typically on short exons) or catalyses back-splicing to generate circular RNA (on long exons). The model is supported by our experiments, which show that an E complex assembled on the middle exon of yeast EFM5 or HMRA1 can be chased into circular RNA when the exon is sufficiently long. This simple model unifies intron definition, exon definition, and back-splicing through the same spliceosome in all eukaryotes and should inspire experiments in many other systems to understand the mechanism and regulation of these processes.
Validation ReportPDB-ID: 6n7r

SummaryFull reportAbout validation report
History
DepositionNov 28, 2018-
Header (metadata) releaseSep 18, 2019-
Map releaseSep 18, 2019-
UpdateOct 2, 2019-
Current statusOct 2, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6n7r
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0361.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 352 pix.
= 478.72 Å
1.36 Å/pix.
x 352 pix.
= 478.72 Å
1.36 Å/pix.
x 352 pix.
= 478.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.15186214 - 0.3124472
Average (Standard dev.)-0.000003998341 (±0.0059512756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 478.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z478.720478.720478.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.1520.312-0.000

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Supplemental data

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Sample components

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Entire Saccharomyces cerevisiae spliceosomal E complex (ACT1)

EntireName: Saccharomyces cerevisiae spliceosomal E complex (ACT1)
Number of components: 20

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Component #1: protein, Saccharomyces cerevisiae spliceosomal E complex (ACT1)

ProteinName: Saccharomyces cerevisiae spliceosomal E complex (ACT1)
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, U1 small nuclear ribonucleoprotein 70 kDa homolog

ProteinName: U1 small nuclear ribonucleoprotein 70 kDa homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.506148 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #3: protein, U1 small nuclear ribonucleoprotein C

ProteinName: U1 small nuclear ribonucleoprotein C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.106016 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #4: protein, U1 small nuclear ribonucleoprotein A

ProteinName: U1 small nuclear ribonucleoprotein A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.413961 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #5: protein, U1 small nuclear ribonucleoprotein component PRP42

ProteinName: U1 small nuclear ribonucleoprotein component PRP42 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.22202 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #6: protein, Pre-mRNA-processing factor 39

ProteinName: Pre-mRNA-processing factor 39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 74.834742 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #7: protein, Protein NAM8

ProteinName: Protein NAM8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.01084 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #8: protein, 56 kDa U1 small nuclear ribonucleoprotein component

ProteinName: 56 kDa U1 small nuclear ribonucleoprotein component / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.575277 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, U1 small nuclear ribonucleoprotein component SNU71,U1 sm...

ProteinName: U1 small nuclear ribonucleoprotein component SNU71,U1 small nuclear ribonucleoprotein component SNU71,Snu71
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.123642 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #10: protein, Protein LUC7

ProteinName: Protein LUC7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.245885 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #11: protein, Small nuclear ribonucleoprotein-associated protein B

ProteinName: Small nuclear ribonucleoprotein-associated protein B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.42699 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #12: protein, Small nuclear ribonucleoprotein Sm D1

ProteinName: Small nuclear ribonucleoprotein Sm D1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.296798 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #13: protein, Small nuclear ribonucleoprotein Sm D2

ProteinName: Small nuclear ribonucleoprotein Sm D2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.876066 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #14: protein, Small nuclear ribonucleoprotein Sm D3

ProteinName: Small nuclear ribonucleoprotein Sm D3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.240139 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #15: protein, Small nuclear ribonucleoprotein E

ProteinName: Small nuclear ribonucleoprotein E / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.385098 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #16: protein, Small nuclear ribonucleoprotein F

ProteinName: Small nuclear ribonucleoprotein F / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.669945 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #17: protein, Small nuclear ribonucleoprotein G

ProteinName: Small nuclear ribonucleoprotein G / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.490809 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #18: nucleic-acid, U1 snRNA

nucleic acidName: U1 snRNAU1 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUACUUACCU UAAGAUAUCA GAGGAGAUCA AGAAGUCCUA CUGAUCAAAC AUGCGCUUCC AAUAGUAGAA GGACGUUAAG CAUUUAUCAU UGAACUAUAA UUGUUCAUUG AAGUCAUUGA UGCAAACUCC UUGGUCACAC ACACAUACGG CGCGGAAGGC GUGUUUGCUG ACGUUUCCAU UCCCUUGUUU CAAUCAUUGG UUAAUCCCUU GAUUCCUUUG GGGAUUUUUG GGUUAAACUG AUUUUUGGGG CCCUUUGUUU CUUCUGCCUG GAGAAGUUUG ACACCAAAUU CAAAUUGGUG UUAGGGGAGC UGGGGCCUUU CAAAAGAGAG CUUUGUAGAG GCAUUCUUUU UGACUACUUU UCUCUAGCGU GCCAUUUUAG UUUUUGACGG CAGAUUCGAA UGAACUUAAG UUUAUGAUGA AGGUAUGGCU GUUGAGAUUA UUUGGUCGGG AUUGUAGUUU GAAGAUGUGC UCUUUUGAGC AGUCUCAACU UUGCUCGUUC CCGUUAUGGG AAAAAUUUUG GAAGGUCUUG GUAGGAACGG GUGGAUCUUA UAAUUUUUGA UUUAUUUU
MassTheoretical: 182.114516 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #19: nucleic-acid, ACT1 pre-mRNA

nucleic acidName: ACT1 pre-mRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGAUCCGAUA UCCGUACACC AUCAGGGUAC GAGCUAGCCC AUGGCGUACA CCAUCAGGGU ACGACUAGUA GAUCUCGUAC ACCAUCAGGG UACGGAAUUG UCUAGACUUU UAGAUUUUUC ACGCUUACUG CUUUUUUCUU CCCAAGAUCG AAAAUUUACU GAAUUAACAA UGGAUUCUGG UAUGUUCNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN
MassTheoretical: 70.171188 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

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Component #20: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.9
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 270587
3D reconstructionSoftware: RELION / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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