+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1846 | |||||||||
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Title | Human native spliceosomal C complex assembled on PM5 pre-mRNA. | |||||||||
Map data | This is a 3D map of the human spliceosomal C complex. | |||||||||
Sample |
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Keywords | spliceosome / pre-mRNA splicing / C complex / catalytically active / PM5 pre-mRNA | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 29.0 Å | |||||||||
Authors | Golas MM / Sander B / Bessonov S / Grote M / Wolf E / Kastner B / Stark H / Luhrmann R | |||||||||
Citation | Journal: Mol Cell / Year: 2010 Title: 3D cryo-EM structure of an active step I spliceosome and localization of its catalytic core. Authors: Monika M Golas / Bjoern Sander / Sergey Bessonov / Michael Grote / Elmar Wolf / Berthold Kastner / Holger Stark / Reinhard Lührmann / Abstract: The spliceosome excises introns from pre-mRNA in a two-step splicing reaction. So far, the three-dimensional (3D) structure of a spliceosome with preserved catalytic activity has remained elusive. ...The spliceosome excises introns from pre-mRNA in a two-step splicing reaction. So far, the three-dimensional (3D) structure of a spliceosome with preserved catalytic activity has remained elusive. Here, we determined the 3D structure of the human, catalytically active step I spliceosome (C complex) by cryo-electron microscopy (cryo-EM) in vitrified ice. Via immunolabeling we mapped the position of the 5' exon. The C complex contains an unusually salt-stable ribonucleoprotein (RNP) core that harbors its catalytic center. We determined the 3D structure of this RNP core and also that of a post-step II particle, the 35S U5 snRNP, which contains most of the C complex core proteins. As C complex domains could be recognized in these structures, their position in the C complex could be determined, thereby allowing the region harboring the spliceosome's catalytic core to be localized. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1846.map.gz | 3.8 MB | EMDB map data format | |
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Header (meta data) | emd-1846-v30.xml emd-1846.xml | 6.6 KB 6.6 KB | Display Display | EMDB header |
Images | emd_1846.png | 89.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1846 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1846 | HTTPS FTP |
-Validation report
Summary document | emd_1846_validation.pdf.gz | 189.1 KB | Display | EMDB validaton report |
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Full document | emd_1846_full_validation.pdf.gz | 188.2 KB | Display | |
Data in XML | emd_1846_validation.xml.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1846 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1846 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1846.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a 3D map of the human spliceosomal C complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human native spliceosomal C complex
Entire | Name: Human native spliceosomal C complex |
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Components |
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-Supramolecule #1000: Human native spliceosomal C complex
Supramolecule | Name: Human native spliceosomal C complex / type: sample / ID: 1000 / Details: Experimental weight in the range of 5-5.5MDa / Number unique components: 1 |
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Molecular weight | Experimental: 5 MDa |
-Supramolecule #1: Human native spliceosomal C complex
Supramolecule | Name: Human native spliceosomal C complex / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Spliceosomal C complex / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Electron beam | Acceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.5 CUT-OFF |
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