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Yorodumi- EMDB-19791: Flexible reconstruction of a pre-catalytic spliceosome (EMPIAR-10... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19791 | |||||||||
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Title | Flexible reconstruction of a pre-catalytic spliceosome (EMPIAR-10180) using DynaMight | |||||||||
Map data | local resolution filtered map from the DynaMight half maps | |||||||||
Sample |
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Keywords | Spliceosome / SPLICING | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.98 Å | |||||||||
Authors | Schwab J / Scheres SHW | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nature / Year: 2017 Title: Structure of a pre-catalytic spliceosome. Authors: Clemens Plaschka / Pei-Chun Lin / Kiyoshi Nagai / Abstract: Intron removal requires assembly of the spliceosome on precursor mRNA (pre-mRNA) and extensive remodelling to form the spliceosome's catalytic centre. Here we report the cryo-electron microscopy ...Intron removal requires assembly of the spliceosome on precursor mRNA (pre-mRNA) and extensive remodelling to form the spliceosome's catalytic centre. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae pre-catalytic B complex spliceosome at near-atomic resolution. The mobile U2 small nuclear ribonucleoprotein particle (snRNP) associates with U4/U6.U5 tri-snRNP through the U2/U6 helix II and an interface between U4/U6 di-snRNP and the U2 snRNP SF3b-containing domain, which also transiently contacts the helicase Brr2. The 3' region of the U2 snRNP is flexibly attached to the SF3b-containing domain and protrudes over the concave surface of tri-snRNP, where the U1 snRNP may reside before its release from the pre-mRNA 5' splice site. The U6 ACAGAGA sequence forms a hairpin that weakly tethers the 5' splice site. The B complex proteins Prp38, Snu23 and Spp381 bind the Prp8 N-terminal domain and stabilize U6 ACAGAGA stem-pre-mRNA and Brr2-U4 small nuclear RNA interactions. These results provide important insights into the events leading to active site formation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19791.map.gz | 70.6 MB | EMDB map data format | |
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Header (meta data) | emd-19791-v30.xml emd-19791.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_19791.png | 79.6 KB | ||
Filedesc metadata | emd-19791.cif.gz | 3.8 KB | ||
Others | emd_19791_half_map_1.map.gz emd_19791_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19791 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19791 | HTTPS FTP |
-Validation report
Summary document | emd_19791_validation.pdf.gz | 922 KB | Display | EMDB validaton report |
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Full document | emd_19791_full_validation.pdf.gz | 921.5 KB | Display | |
Data in XML | emd_19791_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_19791_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19791 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19791 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19791.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | local resolution filtered map from the DynaMight half maps | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.7 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: unfiltered, unmasked half map reconstructed with DynaMight
File | emd_19791_half_map_1.map | ||||||||||||
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Annotation | unfiltered, unmasked half map reconstructed with DynaMight | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unfiltered, unmasked half map reconstructed with DynaMight
File | emd_19791_half_map_2.map | ||||||||||||
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Annotation | unfiltered, unmasked half map reconstructed with DynaMight | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pre-catalytic B complex Spliceosome
Entire | Name: Pre-catalytic B complex Spliceosome |
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Components |
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-Supramolecule #1: Pre-catalytic B complex Spliceosome
Supramolecule | Name: Pre-catalytic B complex Spliceosome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-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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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) / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.3 µm / Nominal defocus min: 0.35000000000000003 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44537 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0) |