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- PDB-6n7p: S. cerevisiae spliceosomal E complex (UBC4) -

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Basic information

Entry
Database: PDB / ID: 6n7p
TitleS. cerevisiae spliceosomal E complex (UBC4)
Components
  • (Nuclear cap-binding protein ...) x 2
  • (Pre-mRNA-processing ...) x 2
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U1 small nuclear ribonucleoprotein ...) x 5
  • 56 kDa U1 small nuclear ribonucleoprotein component
  • Protein LUC7
  • Protein NAM8
  • Small nuclear ribonucleoprotein-associated protein B
  • U1 snRNAU1 spliceosomal RNA
  • UBC4 pre-mRNA
KeywordsRNA BINDING PROTEIN / pre-mRNA splicing / spliceosome / E complex
Function / homology
Function and homology information


Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Processing of Intronless Pre-mRNAs / mRNA Capping / RNA Polymerase II Pre-transcription Events / Formation of the Early Elongation Complex / nuclear cap binding complex / positive regulation of RNA binding / mRNA splice site selection / splicing factor binding ...Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Processing of Intronless Pre-mRNAs / mRNA Capping / RNA Polymerase II Pre-transcription Events / Formation of the Early Elongation Complex / nuclear cap binding complex / positive regulation of RNA binding / mRNA splice site selection / splicing factor binding / positive regulation of mRNA splicing, via spliceosome / RNA cap binding / pICln-Sm protein complex / mRNA 5'-splice site recognition / U4 snRNP / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / mRNA cap binding complex / pre-mRNA 5'-splice site binding / mRNA cis splicing, via spliceosome / commitment complex / U12-type spliceosomal complex / U2 snRNP / small nucleolar ribonucleoprotein complex / U5 snRNP / spliceosomal snRNP assembly / U2-type prespliceosome / P granule / U1 snRNP / U4/U6 x U5 tri-snRNP complex / U1 snRNA binding / poly(U) RNA binding / mRNA transport / 7-methylguanosine mRNA capping / response to osmotic stress / catalytic step 2 spliceosome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / polysome / mRNA splicing, via spliceosome / mRNA binding / perinuclear region of cytoplasm / mitochondrion / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Sm-like protein Lsm6/SmF / MIF4G-like, type 1 / Nuclear cap-binding protein subunit 2 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Small nuclear ribonucleoprotein E / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein C / Armadillo-type fold / MIF4G-like domain superfamily / MIF4G-like, type 2 ...Sm-like protein Lsm6/SmF / MIF4G-like, type 1 / Nuclear cap-binding protein subunit 2 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Small nuclear ribonucleoprotein E / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein C / Armadillo-type fold / MIF4G-like domain superfamily / MIF4G-like, type 2 / U1-C, C2H2-type zinc finger / Small nuclear ribonucleoprotein Sm D2 / Nucleotide-binding alpha-beta plait domain superfamily / Tetratricopeptide-like helical domain superfamily / LSM domain superfamily / Luc7-related / MIF4G-like, type 3 / Matrin/U1-C-like, C2H2-type zinc finger / HAT (Half-A-TPR) repeat / FF domain / Nuclear cap-binding protein subunit 1 / Small nuclear ribonucleoprotein G / WW/rsp5/WWP domain signature. / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / MIF4G like / MIF4G like / U1 zinc finger / LUC7 N_terminus / MIF4G domain / FF domain / LSM domain / WW domain / U1 small nuclear ribonucleoprotein 70kDa / Small nuclear ribonucleoprotein Sm D3 / Pre-mRNA-processing factor Prp40 / FF domain superfamily / Zinc finger C2H2 superfamily / WW domain superfamily / RNA-binding domain superfamily / NCBP2, RNA recognition motif / snRNP70, RNA recognition motif / Small nuclear ribonucleoprotein F / PWI domain / WW domain / LSM domain, eukaryotic/archaea-type / Eukaryotic RNA Recognition Motif (RRM) profile. / FF domain profile. / Zinc finger matrin-type profile. / Matrin/U1-C, C2H2-type zinc finger / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / WW/rsp5/WWP domain profile. / RNA recognition motif domain
U1 small nuclear ribonucleoprotein 70 kDa homolog / Small nuclear ribonucleoprotein E / Nuclear cap-binding protein subunit 2 / 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 G ...U1 small nuclear ribonucleoprotein 70 kDa homolog / Small nuclear ribonucleoprotein E / Nuclear cap-binding protein subunit 2 / 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 G / Protein NAM8 / Small nuclear ribonucleoprotein F / U1 small nuclear ribonucleoprotein component SNU71 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein-associated protein B / Pre-mRNA-processing factor 39 / Nuclear cap-binding protein complex subunit 1 / Pre-mRNA-processing protein PRP40 / U1 small nuclear ribonucleoprotein A / gb:1039023756:
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu, S. / Li, X. / Zhou, Z.H. / Zhao, R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteGM126157 United States
National Institutes of Health/National Human Genome Research InstituteGM114178 United States
National Institutes of Health/National Human Genome Research InstituteGM071940 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 Report
SummaryFull reportAbout validation report
History
DepositionNov 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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,U1 small nuclear ribonucleoprotein component SNU71,Snu71
I: Protein LUC7
J: Pre-mRNA-processing protein PRP40
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
r: UBC4 pre-mRNA
X: Nuclear cap-binding protein complex subunit 1
Y: Nuclear cap-binding protein subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)944,22224
Polymers944,02621
Non-polymers1963
Water0
1


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/peptide 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/peptide 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/peptide U1 small nuclear ribonucleoprotein A / U1A / Mutant U1 die protein 1


Mass: 40413.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain (production host): ATCC 204508 / S288c / References: UniProt: P32605
#4: Protein/peptide 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/peptide U1 small nuclear ribonucleoprotein component SNU71,U1 small nuclear ribonucleoprotein component SNU71,Snu71


Mass: 10485.320 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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Pre-mRNA-processing ... , 2 types, 2 molecules EJ

#5: Protein/peptide 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
#10: Protein/peptide Pre-mRNA-processing protein PRP40


Mass: 69176.016 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: P33203

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Protein/peptide , 4 types, 4 molecules FGIK

#6: Protein/peptide 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/peptide 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/peptide Protein LUC7


Mass: 30245.885 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: Q07508
#11: Protein/peptide 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

#12: Protein/peptide 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
#13: Protein/peptide 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
#14: Protein/peptide 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
#15: Protein/peptide 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
#16: Protein/peptide 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
#17: Protein/peptide 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 , 2 types, 2 molecules Rr

#18: RNA chain U1 snRNA / U1 spliceosomal RNA


Mass: 182114.516 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: GenBank: 1039023756
#19: RNA chain UBC4 pre-mRNA


Mass: 81030.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288C (yeast)

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Nuclear cap-binding protein ... , 2 types, 2 molecules XY

#20: Protein/peptide Nuclear cap-binding protein complex subunit 1 / 80 kDa nuclear cap-binding protein / NCBP 80 kDa subunit / Glycolysis regulation protein 3 / Protein SUT1 / Suppressor of TOP1 protein


Mass: 100115.047 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: P34160
#21: Protein/peptide Nuclear cap-binding protein subunit 2 / 20 kDa nuclear cap-binding protein / NCBP 20 kDa subunit / CBP20


Mass: 23803.467 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: Q08920

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Non-polymers , 1 types, 3 molecules

#22: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Zinc

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Details

Has ligand of interestN

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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: Saccharomyces cerevisiae spliceosomal E complex (EBC4)
Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21
Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (baker's 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 FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND4CTF correction
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
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: 124825 / Symmetry type: POINT

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