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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


: / : / Processing of Intronless Pre-mRNAs / nuclear cap binding complex / positive regulation of RNA binding / RNA cap binding / U4/U6 snRNP / primary miRNA processing / : / splicing factor binding ...: / : / Processing of Intronless Pre-mRNAs / nuclear cap binding complex / positive regulation of RNA binding / RNA cap binding / U4/U6 snRNP / primary miRNA processing / : / splicing factor binding / mRNA splice site recognition / 7-methylguanosine cap hypermethylation / mRNA 3'-end processing / pICln-Sm protein complex / spliceosomal tri-snRNP complex / U4 snRNP / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / : / U2-type prespliceosome assembly / commitment complex / U2 snRNP / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process / U1 snRNP / U2-type prespliceosome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / pre-mRNA 5'-splice site binding / response to osmotic stress / precatalytic spliceosome / spliceosomal complex assembly / Processing of Capped Intron-Containing Pre-mRNA / Formation of the Early Elongation Complex / mRNA Capping / RNA Polymerase II Pre-transcription Events / 7-methylguanosine mRNA capping / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA 5'-splice site recognition / mRNA transport / U5 snRNP / spliceosomal snRNP assembly / mRNA export from nucleus / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / mRNA binding / perinuclear region of cytoplasm / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Luc7-related / LUC7 N_terminus / Snu56-like U1 small nuclear ribonucleoprotein component / Snu56-like U1 small nuclear ribonucleoprotein component / Pre-mRNA-processing factor Prp40 / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / MIF4G-like, type 1 / MIF4G-like, type 2 / U1 small nuclear ribonucleoprotein C ...Luc7-related / LUC7 N_terminus / Snu56-like U1 small nuclear ribonucleoprotein component / Snu56-like U1 small nuclear ribonucleoprotein component / Pre-mRNA-processing factor Prp40 / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / MIF4G-like, type 1 / MIF4G-like, type 2 / U1 small nuclear ribonucleoprotein C / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / 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 / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / SH3 type barrels. - #100 / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / 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 / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / 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 / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Roll / 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 protein PRP40 / Nuclear cap-binding protein complex subunit 1 / Pre-mRNA-processing factor 39 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G ...: / RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein A / Pre-mRNA-processing protein PRP40 / Nuclear cap-binding protein complex subunit 1 / 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 / Protein LUC7 / Nuclear cap-binding protein subunit 2 / 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
AuthorsLiu, S. / Li, X. / Zhou, Z.H. / Zhao, R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM126157 United States
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)GM071940 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI094386 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.
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
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 20, 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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  • Deposited structure unit
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  • EMDB-0360
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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


  • 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: 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 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,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 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 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 , 4 types, 4 molecules FGIK

#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 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 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 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 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 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 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 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 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 Nuclear cap-binding protein complex subunit 1 / 80 kDa nuclear cap-binding protein / NCBP 80 kDa subunit / Glycolysis regulation protein 3 / ...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 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

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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-#21 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer'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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