+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 / RNA cap binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / primary miRNA processing / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP ...: / : / Processing of Intronless Pre-mRNAs / nuclear cap binding complex / RNA cap binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / primary miRNA processing / mRNA splice site recognition / splicing factor binding / U4/U6 snRNP / mRNA 3'-end processing / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / mRNA cis splicing, via spliceosome / commitment complex / poly(U) RNA binding / U2-type prespliceosome assembly / U4 snRNP / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / U1 snRNP / response to osmotic stress / pre-mRNA 5'-splice site binding / U2-type prespliceosome / Processing of Capped Intron-Containing Pre-mRNA / nuclear-transcribed mRNA catabolic process / 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 / mRNA export from nucleus / spliceosomal snRNP assembly / 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 | 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 |
-Validation report
Summary document | emd_0360_validation.pdf.gz | 594.4 KB | Display | EMDB validaton report |
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Full document | emd_0360_full_validation.pdf.gz | 593.9 KB | Display | |
Data in XML | emd_0360_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | emd_0360_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0360 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |