[English] 日本語
Yorodumi- EMDB-1258: Organization of core spliceosomal components U5 snRNA loop I and ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1258 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Organization of core spliceosomal components U5 snRNA loop I and U4/U6 Di-snRNP within U4/U6.U5 Tri-snRNP as revealed by electron cryomicroscopy. | |||||||||
Map data | 3D map of human U5 snRNP | |||||||||
Sample |
| |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 32.0 Å | |||||||||
Authors | Sander B / Golas MM / Kastner B / Luhrmann R / Stark H | |||||||||
Citation | Journal: Mol Cell / Year: 2006 Title: Organization of core spliceosomal components U5 snRNA loop I and U4/U6 Di-snRNP within U4/U6.U5 Tri-snRNP as revealed by electron cryomicroscopy. Authors: Bjoern Sander / Monika M Golas / Evgeny M Makarov / Hero Brahms / Berthold Kastner / Reinhard Lührmann / Holger Stark / Abstract: In eukaryotes, pre-mRNA exons are interrupted by large noncoding introns. Alternative selection of exons and nucleotide-exact removal of introns are performed by the spliceosome, a highly dynamic ...In eukaryotes, pre-mRNA exons are interrupted by large noncoding introns. Alternative selection of exons and nucleotide-exact removal of introns are performed by the spliceosome, a highly dynamic macromolecular machine. U4/U6.U5 tri-snRNP is the largest and most conserved building block of the spliceosome. By 3D electron cryomicroscopy and labeling, the exon-aligning U5 snRNA loop I is localized at the center of the tetrahedrally shaped tri-snRNP reconstructed to approximately 2.1 nm resolution in vitrified ice. Independent 3D reconstructions of its subunits, U4/U6 and U5 snRNPs, show how U4/U6 and U5 combine to form tri-snRNP and, together with labeling experiments, indicate a close proximity of the spliceosomal core components U5 snRNA loop I and U4/U6 at the center of tri-snRNP. We suggest that this central tri-snRNP region may be the site to which the prespliceosomal U2 snRNA has to approach closely during formation of the catalytic core of the spliceosome. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1258.map.gz | 655.8 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-1258-v30.xml emd-1258.xml | 6.1 KB 6.1 KB | Display Display | EMDB header |
Images | 1258.gif | 39.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1258 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1258 | HTTPS FTP |
-Validation report
Summary document | emd_1258_validation.pdf.gz | 193.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_1258_full_validation.pdf.gz | 192.3 KB | Display | |
Data in XML | emd_1258_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1258 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1258 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_1258.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 3D map of human U5 snRNP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Human U5 snRNP
Entire | Name: Human U5 snRNP |
---|---|
Components |
|
-Supramolecule #1000: Human U5 snRNP
Supramolecule | Name: Human U5 snRNP / type: sample / ID: 1000 / Number unique components: 1 |
---|
-Supramolecule #1: Human U5 snRNP
Supramolecule | Name: Human U5 snRNP / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: HeLa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE |
---|
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG/UT |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.5 CUT-OFF |
---|