+Open data
-Basic information
Entry | Database: PDB / ID: 6n7p | |||||||||||||||
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Title | S. cerevisiae spliceosomal E complex (UBC4) | |||||||||||||||
Components |
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Keywords | RNA 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 | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Saccharomyces cerevisiae S288C (yeast) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
Authors | Liu, S. / Li, X. / Zhou, Z.H. / Zhao, R. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6n7p.cif.gz | 1015.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n7p.ent.gz | 754.7 KB | Display | PDB format |
PDBx/mmJSON format | 6n7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/6n7p ftp://data.pdbj.org/pub/pdb/validation_reports/n7/6n7p | HTTPS FTP |
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-Related structure data
Related structure data | 0360MC 0361C 6n7rC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-U1 small nuclear ribonucleoprotein ... , 5 types, 5 molecules ABCDH
#1: Protein | 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 |
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#2: Protein | 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 | 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 | 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 | 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 |
-Pre-mRNA-processing ... , 2 types, 2 molecules EJ
#5: Protein | 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 |
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#10: Protein | 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 |
-Protein , 4 types, 4 molecules FGIK
#6: Protein | 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 |
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#7: Protein | 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 | 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 | 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 |
-Small nuclear ribonucleoprotein ... , 6 types, 6 molecules LMNOPQ
#12: Protein | 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 |
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#13: Protein | 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 | 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 | 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 | 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 | 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 |
-RNA chain , 2 types, 2 molecules Rr
#18: RNA chain | 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 |
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#19: RNA chain | Mass: 81030.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288C (yeast) |
-Nuclear cap-binding protein ... , 2 types, 2 molecules XY
#20: 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 |
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#21: Protein | 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 |
-Non-polymers , 1 types, 3 molecules
#22: Chemical |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Saccharomyces cerevisiae spliceosomal E complex (EBC4) Type: COMPLEX / Entity ID: #1-#21 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124825 / Symmetry type: POINT |