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Open data
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Basic information
Entry | Database: PDB / ID: 6n7p | |||||||||||||||
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Title | S. cerevisiae spliceosomal E complex (UBC4) | |||||||||||||||
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![]() | RNA BINDING PROTEIN / pre-mRNA splicing / spliceosome / E complex | |||||||||||||||
Function / homology | ![]() : / : / Processing of Intronless Pre-mRNAs / nuclear cap binding complex / positive regulation of RNA binding / RNA cap binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / primary miRNA processing / regulation of mRNA processing / mRNA splice site recognition ...: / : / Processing of Intronless Pre-mRNAs / nuclear cap binding complex / positive regulation of RNA binding / RNA cap binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / primary miRNA processing / regulation of mRNA processing / mRNA splice site recognition / splicing factor binding / mRNA 3'-end processing / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / poly(U) RNA binding / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome assembly / U4 snRNP / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / U1 snRNP / response to osmotic stress / pre-mRNA 5'-splice site binding / U2-type prespliceosome / nuclear-transcribed mRNA catabolic process / Processing of Capped Intron-Containing Pre-mRNA / Formation of the Early Elongation Complex / mRNA Capping / RNA Polymerase II Pre-transcription Events / precatalytic spliceosome / spliceosomal complex assembly / 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 / 7-methylguanosine mRNA capping / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
![]() | Liu, S. / Li, X. / Zhou, Z.H. / Zhao, R. | |||||||||||||||
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1015.9 KB | Display | ![]() |
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PDB format | ![]() | 754.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 117 KB | Display | |
Data in CIF | ![]() | 194.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0360MC ![]() 0361C ![]() 6n7rC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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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) ![]() ![]() 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) ![]() ![]() 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.) ![]() ![]() Strain: ATCC 204508 / S288c Production host: ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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.) ![]() ![]() |
-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) ![]() ![]() 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) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q08920 |
-Non-polymers , 1 types, 3 molecules ![](data/chem/img/ZN.gif)
#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 |
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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: ![]() ![]() |
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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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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 |