+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0360 | |||||||||||||||
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Title | Saccharomyces cerevisiae spliceosomal E complex (UBC4) | |||||||||||||||
Map data | Spliceosomal E complex (UBC4) | |||||||||||||||
Sample |
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Keywords | pre-mRNA splicing / spliceosome / E complex / RNA BINDING PROTEIN | |||||||||||||||
Function / homology | Function and homology information : / : / Processing of Intronless Pre-mRNAs / nuclear cap binding complex / positive regulation of RNA binding / RNA cap binding / primary miRNA processing / : / splicing factor binding / mRNA splice site recognition ...: / : / Processing of Intronless Pre-mRNAs / nuclear cap binding complex / positive regulation of RNA binding / RNA cap binding / primary miRNA processing / : / splicing factor binding / mRNA splice site recognition / U4/U6 snRNP / : / 7-methylguanosine cap hypermethylation / mRNA 3'-end processing / pICln-Sm protein complex / spliceosomal tri-snRNP complex / 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 / U4 snRNP / 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 / Processing of Capped Intron-Containing Pre-mRNA / Formation of the Early Elongation Complex / mRNA Capping / spliceosomal complex assembly / 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 (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
Authors | Liu S / Li X | |||||||||||||||
Funding support | United States, 4 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0360.map.gz | 199.6 MB | EMDB map data format | |
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Header (meta data) | emd-0360-v30.xml emd-0360.xml | 37.2 KB 37.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0360_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_0360.png | 46.3 KB | ||
Filedesc metadata | emd-0360.cif.gz | 10.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0360 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0360 | HTTPS FTP |
-Related structure data
Related structure data | 6n7pMC 0361C 6n7rC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0360.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Spliceosomal E complex (UBC4) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Saccharomyces cerevisiae spliceosomal E complex (EBC4)
+Supramolecule #1: Saccharomyces cerevisiae spliceosomal E complex (EBC4)
+Macromolecule #1: U1 small nuclear ribonucleoprotein 70 kDa homolog
+Macromolecule #2: U1 small nuclear ribonucleoprotein C
+Macromolecule #3: U1 small nuclear ribonucleoprotein A
+Macromolecule #4: U1 small nuclear ribonucleoprotein component PRP42
+Macromolecule #5: Pre-mRNA-processing factor 39
+Macromolecule #6: Protein NAM8
+Macromolecule #7: 56 kDa U1 small nuclear ribonucleoprotein component
+Macromolecule #8: U1 small nuclear ribonucleoprotein component SNU71,U1 small nucle...
+Macromolecule #9: Protein LUC7
+Macromolecule #10: Pre-mRNA-processing protein PRP40
+Macromolecule #11: Small nuclear ribonucleoprotein-associated protein B
+Macromolecule #12: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #13: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #14: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #15: Small nuclear ribonucleoprotein E
+Macromolecule #16: Small nuclear ribonucleoprotein F
+Macromolecule #17: Small nuclear ribonucleoprotein G
+Macromolecule #20: Nuclear cap-binding protein complex subunit 1
+Macromolecule #21: Nuclear cap-binding protein subunit 2
+Macromolecule #18: U1 snRNA
+Macromolecule #19: UBC4 pre-mRNA
+Macromolecule #22: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |