[English] 日本語
Yorodumi- EMDB-0684: Cryo-EM structure of the catalytic activated yeast spliceosome (B... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0684 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the catalytic activated yeast spliceosome (B* complex) assembled on ACT1 pre-mRNA at 2.9 angstrom resolution | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Wan R / Bai R / Yan C / Lei J / Shi Y | |||||||||
Citation | Journal: Cell / Year: 2019 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0684.map.gz | 227.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-0684-v30.xml emd-0684.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd_0684.png | 237.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0684 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0684 | HTTPS FTP |
-Validation report
Summary document | emd_0684_validation.pdf.gz | 79 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_0684_full_validation.pdf.gz | 78.1 KB | Display | |
Data in XML | emd_0684_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0684 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0684 | HTTPS FTP |
-Related structure data
Related structure data | 0685C 0686C 0687C 0691C 0692C 6j6gC 6j6hC 6j6nC 6j6qC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_0684.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : the catalytic activated spliceosome B* complex assembled on ACT1 ...
Entire | Name: the catalytic activated spliceosome B* complex assembled on ACT1 pre-mRNA |
---|---|
Components |
|
-Supramolecule #1: the catalytic activated spliceosome B* complex assembled on ACT1 ...
Supramolecule | Name: the catalytic activated spliceosome B* complex assembled on ACT1 pre-mRNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |