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Yorodumi- EMDB-19789: Flexible reconstruction of the yeast U4/U6.U5 tri-snRNP (EMPIAR-1... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19789 | |||||||||
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Title | Flexible reconstruction of the yeast U4/U6.U5 tri-snRNP (EMPIAR-10073) using DynaMight | |||||||||
Map data | local resolution filtered map from the DynaMight half maps. Reconstruction was done with a subset of 86,624 particles of EMPIAR-10073 with deformation correction | |||||||||
Sample |
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Keywords | Spliceosome / SPLICING | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.91 Å | |||||||||
Authors | Schwab J / Scheres SHW | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nature / Year: 2016 Title: Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution. Authors: Thi Hoang Duong Nguyen / Wojciech P Galej / Xiao-Chen Bai / Chris Oubridge / Andrew J Newman / Sjors H W Scheres / Kiyoshi Nagai / Abstract: U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led ...U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryo-electron microscopy structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7 Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 small nuclear RNAs (snRNAs). The structure reveals striking interweaving interactions of the protein and RNA components, including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin stabilized by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP, but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in the amino-terminal domain of Prp8. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19789.map.gz | 5.2 MB | EMDB map data format | |
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Header (meta data) | emd-19789-v30.xml emd-19789.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
Images | emd_19789.png | 128.7 KB | ||
Filedesc metadata | emd-19789.cif.gz | 4 KB | ||
Others | emd_19789_half_map_1.map.gz emd_19789_half_map_2.map.gz | 194.7 MB 194.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19789 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19789 | HTTPS FTP |
-Validation report
Summary document | emd_19789_validation.pdf.gz | 815.7 KB | Display | EMDB validaton report |
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Full document | emd_19789_full_validation.pdf.gz | 815.3 KB | Display | |
Data in XML | emd_19789_validation.xml.gz | 15 KB | Display | |
Data in CIF | emd_19789_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19789 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19789 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19789.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | local resolution filtered map from the DynaMight half maps. Reconstruction was done with a subset of 86,624 particles of EMPIAR-10073 with deformation correction | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.40001 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Unfiltered half map obtained with DynaMight reconstruction
File | emd_19789_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map obtained with DynaMight reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map obtained with DynaMight reconstruction
File | emd_19789_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map obtained with DynaMight reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP
Entire | Name: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP |
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Components |
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-Supramolecule #1: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP
Supramolecule | Name: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP 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: NITROGEN |
-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: 38.0 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: 3.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |