+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1594 | |||||||||
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Title | 35-40S RNA editing complex of Trypanosoma brucei | |||||||||
Map data | 3D map of the 35-40S RNA editing complex of Trypanosoma brucei | |||||||||
Sample |
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Keywords | RNA editing / Trypanosoma brucei | |||||||||
Biological species | Trypanosoma brucei (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 19.0 Å | |||||||||
Authors | Golas MM / Boehm C / Sander B / Effenberger K / Brecht M / Stark H / Goeringer HU | |||||||||
Citation | Journal: EMBO J / Year: 2009 Title: Snapshots of the RNA editing machine in trypanosomes captured at different assembly stages in vivo. Authors: Monika M Golas / Cordula Böhm / Bjoern Sander / Kerstin Effenberger / Michael Brecht / Holger Stark / H Ulrich Göringer / Abstract: Mitochondrial pre-messenger RNAs in kinetoplastid protozoa are substrates of uridylate-specific RNA editing. RNA editing converts non-functional pre-mRNAs into translatable molecules and can generate ...Mitochondrial pre-messenger RNAs in kinetoplastid protozoa are substrates of uridylate-specific RNA editing. RNA editing converts non-functional pre-mRNAs into translatable molecules and can generate protein diversity by alternative editing. Although several editing complexes have been described, their structure and relationship is unknown. Here, we report the isolation of functionally active RNA editing complexes by a multistep purification procedure. We show that the endogenous isolates contain two subpopulations of approximately 20S and approximately 35-40S and present the three-dimensional structures of both complexes by electron microscopy. The approximately 35-40S complexes consist of a platform density packed against a semispherical element. The approximately 20S complexes are composed of two subdomains connected by an interface. The two particles are structurally related, and we show that RNA binding is a main determinant for the interconversion of the two complexes. The approximately 20S editosomes contain an RNA-binding site, which binds gRNA, pre-mRNA and gRNA/pre-mRNA hybrid molecules with nanomolar affinity. Variability analysis indicates that subsets of complexes lack or possess additional domains, suggesting binding sites for components. Together, a picture of the RNA editing machinery is provided. | |||||||||
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_1594.map.gz | 14.4 MB | EMDB map data format | |
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Header (meta data) | emd-1594-v30.xml emd-1594.xml | 6.5 KB 6.5 KB | Display Display | EMDB header |
Images | emd-1594.jpg | 57.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1594 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1594 | HTTPS FTP |
-Validation report
Summary document | emd_1594_validation.pdf.gz | 194.4 KB | Display | EMDB validaton report |
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Full document | emd_1594_full_validation.pdf.gz | 193.6 KB | Display | |
Data in XML | emd_1594_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1594 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1594 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1594.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D map of the 35-40S RNA editing complex of Trypanosoma brucei | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.7 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 : 35-40S RNA editing complex
Entire | Name: 35-40S RNA editing complex |
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Components |
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-Supramolecule #1000: 35-40S RNA editing complex
Supramolecule | Name: 35-40S RNA editing complex / type: sample / ID: 1000 / Details: 1.45 +/- 0.15MDa / Number unique components: 1 |
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Molecular weight | Experimental: 1.45 MDa |
-Supramolecule #1: 35-40S RNA editing complex
Supramolecule | Name: 35-40S RNA editing complex / type: organelle_or_cellular_component / ID: 1 / Name.synonym: editosome / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Trypanosoma brucei (eukaryote) / synonym: trypanosome / Cell: Trypanosoma brucei / Organelle: mitochondrium |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: NITROGEN / 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: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF |
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