+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2966 | |||||||||
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Title | EM structure of the yeast spliceosomal U4/U6.U5 tri-snRNP | |||||||||
Map data | Reconstruction of the yeast U4/U6.U5 tri-snRNP | |||||||||
Sample |
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Keywords | Spliceosome / tri-snRNP | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.9 Å | |||||||||
Authors | Nguyen THD / Galej WP / Bai X-C / Savva CG / Newman AJ / Scheres SHW / Nagai K | |||||||||
Citation | Journal: Nature / Year: 2015 Title: The architecture of the spliceosomal U4/U6.U5 tri-snRNP. Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-chen Bai / Christos G Savva / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai / Abstract: U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key ...U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key components Prp8, Brr2 and Snu114. The tri-snRNP combines with a precursor messenger RNA substrate bound to U1 and U2 small nuclear ribonucleoprotein particles (snRNPs), and transforms into a catalytically active spliceosome after extensive compositional and conformational changes triggered by unwinding of the U4 and U6 (U4/U6) snRNAs. Here we use cryo-electron microscopy single-particle reconstruction of Saccharomyces cerevisiae tri-snRNP at 5.9 Å resolution to reveal the essentially complete organization of its RNA and protein components. The single-stranded region of U4 snRNA between its 3' stem-loop and the U4/U6 snRNA stem I is loaded into the Brr2 helicase active site ready for unwinding. Snu114 and the amino-terminal domain of Prp8 position U5 snRNA to insert its loop I, which aligns the exons for splicing, into the Prp8 active site cavity. The structure provides crucial insights into the activation process and the active site of the spliceosome. | |||||||||
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_2966.map.gz | 78.4 MB | EMDB map data format | |
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Header (meta data) | emd-2966-v30.xml emd-2966.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_2966_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_2966.png | 69 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2966 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2966 | HTTPS FTP |
-Validation report
Summary document | emd_2966_validation.pdf.gz | 284.8 KB | Display | EMDB validaton report |
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Full document | emd_2966_full_validation.pdf.gz | 284 KB | Display | |
Data in XML | emd_2966_validation.xml.gz | 11.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2966 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2966 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2966.map.gz / Format: CCP4 / Size: 81.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the yeast U4/U6.U5 tri-snRNP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.77 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 : Yeast U4/U6.U5 tri-snRNP
Entire | Name: Yeast U4/U6.U5 tri-snRNP |
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Components |
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-Supramolecule #1000: Yeast U4/U6.U5 tri-snRNP
Supramolecule | Name: Yeast U4/U6.U5 tri-snRNP / type: sample / ID: 1000 / Number unique components: 4 |
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Molecular weight | Theoretical: 1.5 MDa |
-Macromolecule #1: U4 snRNA
Macromolecule | Name: U4 snRNA / type: rna / ID: 1 / Classification: OTHER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: budding yeast |
-Macromolecule #2: U5 snRNA
Macromolecule | Name: U5 snRNA / type: rna / ID: 2 / Classification: OTHER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: budding yeast |
-Macromolecule #3: U6 snRNA
Macromolecule | Name: U6 snRNA / type: rna / ID: 3 / Classification: OTHER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: budding yeast |
-Macromolecule #4: U4/U6.U5 tri-snRNP
Macromolecule | Name: U4/U6.U5 tri-snRNP / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Budding yeast / Organelle: Nucleus |