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- EMDB-0685: Cryo-EM structure of the catalytic activated yeast spliceosome (B... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0685 | |||||||||
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Title | Cryo-EM structure of the catalytic activated yeast spliceosome (B* complex) assembled on UBC4 pre-mRNA at 3.2 angstrom resolution | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Wan R / Bai R / Yan C / Lei J / Shi Y | |||||||||
![]() | ![]() Title: Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Authors: Ruixue Wan / Rui Bai / Chuangye Yan / Jianlin Lei / Yigong Shi / ![]() Abstract: Pre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B) is pivotal for understanding the branching reaction. In this study, we ...Pre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B) is pivotal for understanding the branching reaction. In this study, we assembled the B complexes on two different pre-mRNAs from Saccharomyces cerevisiae and determined the cryo-EM structures of four distinct B complexes at overall resolutions of 2.9-3.8 Å. The duplex between U2 small nuclear RNA (snRNA) and the branch point sequence (BPS) is discretely away from the 5'-splice site (5'SS) in the three B complexes that are devoid of the step I splicing factors Yju2 and Cwc25. Recruitment of Yju2 into the active site brings the U2/BPS duplex into the vicinity of 5'SS, with the BPS nucleophile positioned 4 Å away from the catalytic metal M2. This analysis reveals the functional mechanism of Yju2 and Cwc25 in branching. These structures on different pre-mRNAs reveal substrate-specific conformations of the spliceosome in a major functional state. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 224.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.4 KB 8.4 KB | Display Display | ![]() |
Images | ![]() | 57.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 79.1 KB | Display | ![]() |
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Full document | ![]() | 78.1 KB | Display | |
Data in XML | ![]() | 493 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0684C ![]() 0686C ![]() 0687C ![]() 0691C ![]() 0692C ![]() 6j6gC ![]() 6j6hC ![]() 6j6nC ![]() 6j6qC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : the catalytic activated spliceosome B* complex assembled on UBC4 ...
Entire | Name: the catalytic activated spliceosome B* complex assembled on UBC4 pre-mRNA |
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Components |
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-Supramolecule #1: the catalytic activated spliceosome B* complex assembled on UBC4 ...
Supramolecule | Name: the catalytic activated spliceosome B* complex assembled on UBC4 pre-mRNA type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 49.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |