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Yorodumi- EMDB-10140: Post-catalytic P complex spliceosome at 3.3 angstrom resolution f... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10140 | |||||||||
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Title | Post-catalytic P complex spliceosome at 3.3 angstrom resolution from merging data sets | |||||||||
Map data | None | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Wilkinson ME / Nagai K | |||||||||
Funding support | United Kingdom, Belgium, 2 items
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Citation | Journal: Science / Year: 2017 Title: Postcatalytic spliceosome structure reveals mechanism of 3'-splice site selection. Authors: Max E Wilkinson / Sebastian M Fica / Wojciech P Galej / Christine M Norman / Andrew J Newman / Kiyoshi Nagai / Abstract: Introns are removed from eukaryotic messenger RNA precursors by the spliceosome in two transesterification reactions-branching and exon ligation. The mechanism of 3'-splice site recognition during ...Introns are removed from eukaryotic messenger RNA precursors by the spliceosome in two transesterification reactions-branching and exon ligation. The mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3.7-angstrom cryo-electron microscopy structure of the yeast P-complex spliceosome immediately after exon ligation. The 3'-splice site AG dinucleotide is recognized through non-Watson-Crick pairing with the 5' splice site and the branch-point adenosine. After the branching reaction, protein factors work together to remodel the spliceosome and stabilize a conformation competent for 3'-splice site docking, thereby promoting exon ligation. The structure accounts for the strict conservation of the GU and AG dinucleotides at the 5' and 3' ends of introns and provides insight into the catalytic mechanism of exon ligation. | |||||||||
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_10140.map.gz | 395.7 MB | EMDB map data format | |
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Header (meta data) | emd-10140-v30.xml emd-10140.xml | 14 KB 14 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10140_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_10140.png | 105 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10140 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10140 | HTTPS FTP |
-Validation report
Summary document | emd_10140_validation.pdf.gz | 310.8 KB | Display | EMDB validaton report |
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Full document | emd_10140_full_validation.pdf.gz | 309.9 KB | Display | |
Data in XML | emd_10140_validation.xml.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10140 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10140 | HTTPS FTP |
-Related structure data
Similar structure data | |
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EM raw data | EMPIAR-10298 (Title: Yeast postcatalytic spliceosome, two cryoEM data sets at different magnifications Data size: 6.3 TB Data #1: Unaligned movies of P-complex spliceosome at 105,000x magnification (Dataset 1) [micrographs - multiframe] Data #2: Unaligned movies of P-complex spliceosome at 130,000x magnification (Dataset 2) [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10140.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 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 : P complex spliceosome with 3' exon docked
Entire | Name: P complex spliceosome with 3' exon docked |
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Components |
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-Supramolecule #1: P complex spliceosome with 3' exon docked
Supramolecule | Name: P complex spliceosome with 3' exon docked / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 2.2 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.4 mg/mL | ||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 7.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III Details: 3 uL sample was applied to the grid, left for 30s, then blotted for 3s and immediately plunged into liquid ethane. |
-Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Image recording | Image recording ID: 1 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2384 / Average exposure time: 12.0 sec. / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #1~
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Image recording | #0 - Image recording ID: 2 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Number grids imaged: 1 / #0 - Number real images: 173 / #0 - Average exposure time: 7.0 sec. / #0 - Average electron dose: 45.0 e/Å2 / #1 - Image recording ID: 3 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: COUNTING / #1 - Digitization - Frames/image: 1-35 / #1 - Number grids imaged: 1 / #1 - Number real images: 1441 / #1 - Average exposure time: 7.0 sec. / #1 - Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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