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- EMDB-12117: Yeast C complex spliceosome, overall map after focused classifica... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12117 | |||||||||
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Title | Yeast C complex spliceosome, overall map after focused classification on U5 Sm ring | |||||||||
![]() | Yeast C complex spliceosome, overall map after focused classification on U5 Sm ring | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.13 Å | |||||||||
![]() | Wilkinson ME / Fica SM / Galej WP / Nagai K | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for conformational equilibrium of the catalytic spliceosome. Authors: Max E Wilkinson / Sebastian M Fica / Wojciech P Galej / Kiyoshi Nagai / ![]() Abstract: The ATPase Prp16 governs equilibrium between the branching (B/C) and exon ligation (C/P) conformations of the spliceosome. Here, we present the electron cryomicroscopy reconstruction of the ...The ATPase Prp16 governs equilibrium between the branching (B/C) and exon ligation (C/P) conformations of the spliceosome. Here, we present the electron cryomicroscopy reconstruction of the Saccharomyces cerevisiae C-complex spliceosome at 2.8 Å resolution and identify a novel C-complex intermediate (C) that elucidates the molecular basis for this equilibrium. The exon-ligation factors Prp18 and Slu7 bind to C before ATP hydrolysis by Prp16 can destabilize the branching conformation. Biochemical assays suggest that these pre-bound factors prime the C complex for conversion to C by Prp16. A complete model of the Prp19 complex (NTC) reveals how the branching factors Yju2 and Isy1 are recruited by the NTC before branching. Prp16 remodels Yju2 binding after branching, allowing Yju2 to remain tethered to the NTC in the C complex to promote exon ligation. Our results explain how Prp16 action modulates the dynamic binding of step-specific factors to alternatively stabilize the C or C conformation and establish equilibrium of the catalytic spliceosome. #1: ![]() Title: Structural basis for conformational equilibrium of the catalytic spliceosome Authors: Wilkinson ME / Fica SM / Galej WP / Nagai K | |||||||||
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 | ![]() | 224.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.3 KB 19.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 114.7 KB | ||
Others | ![]() ![]() | 182.5 MB 182.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b9vC C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data #1: Unaligned movies of C-complex spliceosome with 3' splice site AG to AC mutation (Dataset 1) [micrographs - multiframe] Data #2: Unaligned movies of C and C*-complex spliceosomes with 3' splice site AG to AdG mutation (Dataset 2) [micrographs - multiframe] Data #3: Unaligned movies of C and C*-complex spliceosomes with 3' splice site AG to AdG mutation (Dataset 3) [micrographs - multiframe] Data #4: Aligned movies of C-complex spliceosomes with cold-sensitive prp16-302 mutation, purified with Cwc25 (Dataset 4) [micrographs - multiframe] Data #5: Unaligned movies of C-complex spliceosomes with cold-sensitive prp16-302 mutation, purified with Cwc25 and incubated with ATP and Mg (Dataset 5) [micrographs - multiframe] Data #6: Unaligned movies of C, C*, and P-complex spliceosomes with dominant-negative Prp22 mutation K512A, purified with Slu7 (Dataset 6) [micrographs - multiframe] Data #7: Unaligned movies of P-complex spliceosomes with dominant-negative Prp22 mutation K512A, treated with anti-3'exon RNaseH oligo, purified in presence of Mg (Dataset 9) [micrographs - single frame] Data #8: Selected C-complex particles after polishing [picked particles - single frame - processed] Data #9: Selected P-complex particles after polishing [picked particles - single frame - processed] Data #10: Various signal subtractions for C- and P-complex spliceosomes [picked particles - single frame - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Yeast C complex spliceosome, overall map after focused classification on U5 Sm ring | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.145 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Yeast C complex spliceosome, overall map after focused...
File | emd_12117_half_map_1.map | ||||||||||||
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Annotation | Yeast C complex spliceosome, overall map after focused classification on U5 Sm ring, half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Yeast C complex spliceosome, overall map after focused...
File | emd_12117_half_map_2.map | ||||||||||||
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Annotation | Yeast C complex spliceosome, overall map after focused classification on U5 Sm ring, half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Yeast C complex spliceosome with Prp18/Slu7 bound
Entire | Name: Yeast C complex spliceosome with Prp18/Slu7 bound |
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Components |
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-Supramolecule #1: Yeast C complex spliceosome with Prp18/Slu7 bound
Supramolecule | Name: Yeast C complex spliceosome with Prp18/Slu7 bound / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#40 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 2 MDa |
-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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Grid | Model: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
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) / Number grids imaged: 9 / Number real images: 24115 / Average electron dose: 40.0 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 |