[English] 日本語
Yorodumi- EMDB-24094: Continuous movement of the pre-catalytic spliceosome, mode 1-2. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24094 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Continuous movement of the pre-catalytic spliceosome, mode 1-2. | |||||||||
Map data | Continuous movement of the pre-catalytic spliceosome, mode 1-2. | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information Sm-like protein family complex / maturation of 5S rRNA / spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / Lsm1-7-Pat1 complex / U6 snRNP / snoRNA guided rRNA 2'-O-methylation / positive regulation of RNA binding / box C/D sno(s)RNA 3'-end processing ...Sm-like protein family complex / maturation of 5S rRNA / spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / Lsm1-7-Pat1 complex / U6 snRNP / snoRNA guided rRNA 2'-O-methylation / positive regulation of RNA binding / box C/D sno(s)RNA 3'-end processing / generation of catalytic spliceosome for first transesterification step / deadenylation-dependent decapping of nuclear-transcribed mRNA / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / box C/D methylation guide snoRNP complex / splicing factor binding / U4/U6 snRNP / P-body assembly / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process / U1 snRNP / U3 snoRNA binding / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / spliceosomal complex assembly / generation of catalytic spliceosome for second transesterification step / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / pre-mRNA intronic binding / maturation of SSU-rRNA / U1 snRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / small-subunit processome / P-body / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / metallopeptidase activity / cytosolic large ribosomal subunit / RNA helicase activity / nucleic acid binding / RNA helicase / response to xenobiotic stimulus / mRNA binding / GTPase activity / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.0 Å | |||||||||
Authors | Chen M / Ludtke SJ | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Nat Methods / Year: 2021 Title: Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM. Authors: Muyuan Chen / Steven J Ludtke / Abstract: Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. Cryogenic electron microscopy (cryo-EM) provides direct visualization of individual ...Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. Cryogenic electron microscopy (cryo-EM) provides direct visualization of individual macromolecules sampling different conformational and compositional states. While numerous methods are available for computational classification of discrete states, characterization of continuous conformational changes or large numbers of discrete state without human supervision remains challenging. Here we present e2gmm, a machine learning algorithm to determine a conformational landscape for proteins or complexes using a three-dimensional Gaussian mixture model mapped onto two-dimensional particle images in known orientations. Using a deep neural network architecture, e2gmm can automatically resolve the structural heterogeneity within the protein complex and map particles onto a small latent space describing conformational and compositional changes. This system presents a more intuitive and flexible representation than other manifold methods currently in use. We demonstrate this method on both simulated data and three biological systems to explore compositional and conformational changes at a range of scales. The software is distributed as part of EMAN2. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24094.map.gz | 7.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-24094-v30.xml emd-24094.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
Images | emd_24094.png | 127.9 KB | ||
Others | emd_24094_additional_1.map.gz emd_24094_additional_2.map.gz emd_24094_additional_3.map.gz emd_24094_additional_4.map.gz emd_24094_additional_5.map.gz | 7.5 MB 7.3 MB 7.3 MB 7.4 MB 7.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24094 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24094 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_24094.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Continuous movement of the pre-catalytic spliceosome, mode 1-2. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.2475 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Continuous movement of the pre-catalytic spliceosome, mode 1-2,...
File | emd_24094_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Continuous movement of the pre-catalytic spliceosome, mode 1-2, frame 3. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Continuous movement of the pre-catalytic spliceosome, mode 1-2,...
File | emd_24094_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Continuous movement of the pre-catalytic spliceosome, mode 1-2, frame 2. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Continuous movement of the pre-catalytic spliceosome, mode 1-2,...
File | emd_24094_additional_3.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Continuous movement of the pre-catalytic spliceosome, mode 1-2, frame 5. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Continuous movement of the pre-catalytic spliceosome, mode 1-2,...
File | emd_24094_additional_4.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Continuous movement of the pre-catalytic spliceosome, mode 1-2, frame 4. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Continuous movement of the pre-catalytic spliceosome, mode 1-2,...
File | emd_24094_additional_5.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Continuous movement of the pre-catalytic spliceosome, mode 1-2, frame 1. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Pre-catalytic spliceosome
Entire | Name: Pre-catalytic spliceosome |
---|---|
Components |
|
-Supramolecule #1: Pre-catalytic spliceosome
Supramolecule | Name: Pre-catalytic spliceosome / type: complex / ID: 1 / Parent: 0 Details: Re-processing of the dataset EMPIAR-10180 to resolve the continuous movement of the system. Five frames of the first motion mode are attached as additional map files. |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
Details | Re-processing of EMPIAR-10180. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
---|---|
Initial angle assignment | Type: NOT APPLICABLE |
Final 3D classification | Software - Name: EMAN (ver. 2.91) / Details: Deep learning based manifold embedding |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: EMAN (ver. 2.91) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: EMAN (ver. 2.91) Details: Each 3D frame of the continuous movement movie includes 4000 particles. The maps are filtered to 20A for visualization. Number images used: 4000 |