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Yorodumi- EMDB-2239: Cryo-electron microscopy structure of the Trypanosoma brucei 80S ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2239 | |||||||||
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Title | Cryo-electron microscopy structure of the Trypanosoma brucei 80S ribosome | |||||||||
Map data | Trypanosoma Brucei 80S Ribosome cryo-em reconstruction filtered according to the local FSC at 0.5 | |||||||||
Sample |
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Keywords | Trypanosoma / brucei / 80S / ribosome / eukaryotic / kinetoplastids / expansion segments / high-resolution | |||||||||
Function / homology | Function and homology information organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / mitochondrial large ribosomal subunit / phosphate ion binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / mitochondrial large ribosomal subunit / phosphate ion binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / regulation of cell growth / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / regulation of cell population proliferation / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Trypanosoma brucei (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.57 Å | |||||||||
Authors | Hashem Y / des Georges A / Fu J / Buss SN / Jossinet F / Jobe A / Zhang Q / Liao HY / Grassucci B / Bajaj C ...Hashem Y / des Georges A / Fu J / Buss SN / Jossinet F / Jobe A / Zhang Q / Liao HY / Grassucci B / Bajaj C / Westhof E / Madison-Antenucci S / Frank J | |||||||||
Citation | Journal: Nature / Year: 2013 Title: High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Authors: Yaser Hashem / Amedee des Georges / Jie Fu / Sarah N Buss / Fabrice Jossinet / Amy Jobe / Qin Zhang / Hstau Y Liao / Robert A Grassucci / Chandrajit Bajaj / Eric Westhof / Susan Madison- ...Authors: Yaser Hashem / Amedee des Georges / Jie Fu / Sarah N Buss / Fabrice Jossinet / Amy Jobe / Qin Zhang / Hstau Y Liao / Robert A Grassucci / Chandrajit Bajaj / Eric Westhof / Susan Madison-Antenucci / Joachim Frank / Abstract: Ribosomes, the protein factories of living cells, translate genetic information carried by messenger RNAs into proteins, and are thus involved in virtually all aspects of cellular development and ...Ribosomes, the protein factories of living cells, translate genetic information carried by messenger RNAs into proteins, and are thus involved in virtually all aspects of cellular development and maintenance. The few available structures of the eukaryotic ribosome reveal that it is more complex than its prokaryotic counterpart, owing mainly to the presence of eukaryote-specific ribosomal proteins and additional ribosomal RNA insertions, called expansion segments. The structures also differ among species, partly in the size and arrangement of these expansion segments. Such differences are extreme in kinetoplastids, unicellular eukaryotic parasites often infectious to humans. Here we present a high-resolution cryo-electron microscopy structure of the ribosome of Trypanosoma brucei, the parasite that is transmitted by the tsetse fly and that causes African sleeping sickness. The atomic model reveals the unique features of this ribosome, characterized mainly by the presence of unusually large expansion segments and ribosomal-protein extensions leading to the formation of four additional inter-subunit bridges. We also find additional rRNA insertions, including one large rRNA domain that is not found in other eukaryotes. Furthermore, the structure reveals the five cleavage sites of the kinetoplastid large ribosomal subunit (LSU) rRNA chain, which is known to be cleaved uniquely into six pieces, and suggests that the cleavage is important for the maintenance of the T. brucei ribosome in the observed structure. We discuss several possible implications of the large rRNA expansion segments for the translation-regulation process. The structure could serve as a basis for future experiments aimed at understanding the functional importance of these kinetoplastid-specific ribosomal features in protein-translation regulation, an essential step towards finding effective and safe kinetoplastid-specific drugs. | |||||||||
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_2239.map.gz | 7 MB | EMDB map data format | |
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Header (meta data) | emd-2239-v30.xml emd-2239.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_2239_fsc.xml | 22.9 KB | Display | FSC data file |
Images | emd_2239.jpg | 59.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2239 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2239 | HTTPS FTP |
-Validation report
Summary document | emd_2239_validation.pdf.gz | 285.1 KB | Display | EMDB validaton report |
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Full document | emd_2239_full_validation.pdf.gz | 284.2 KB | Display | |
Data in XML | emd_2239_validation.xml.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2239 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2239 | HTTPS FTP |
-Related structure data
Related structure data | 4v8mMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2239.map.gz / Format: CCP4 / Size: 172.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Trypanosoma Brucei 80S Ribosome cryo-em reconstruction filtered according to the local FSC at 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 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 : Trypanosoma Brucei 80S Ribosome
Entire | Name: Trypanosoma Brucei 80S Ribosome |
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Components |
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-Supramolecule #1000: Trypanosoma Brucei 80S Ribosome
Supramolecule | Name: Trypanosoma Brucei 80S Ribosome / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 3.305 MDa Method: Molecular weight estimated form the protein and RNA sequence. |
-Supramolecule #1: 80S Ribosome
Supramolecule | Name: 80S Ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Trypanosoma brucei (eukaryote) / Strain: TREU 667 / Location in cell: Cytoplasm |
Molecular weight | Theoretical: 3.3 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.105 mg/mL |
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Buffer | pH: 7.2 Details: 20 mM Tris pH 7.2, 100mM MgCl2, 500 mM KCl, 5 mM beta-mercaptoethanol |
Grid | Details: 300 mesh Copper/Molbydenum holey carbon-coated Quantifoil 2/4 grid (Quantifoil Micro Tools GmbH) containing an additional continuous thin layer of carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV / Method: Wait 30 sec, Blot 6 seconds, plunge |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Jan 1, 2011 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Number real images: 1000 / Average electron dose: 25 e/Å2 / Bits/pixel: 32 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: 3u5b |
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Software | Name: Chimera |
Details | Protocol: Rigid body. The structure of the 80S from Yeast (3U5B and others) as well as the structure of the 60S from Tetrahymena thermophila (4A17 and others) were used as starting model for the 60S subunit model. The 40S from Tetrahymena thermophila (2XZM and 2XZN) as well as the 80S from Yeast were used as starting model for the 40S subunit model. The 80S model of Triticum aestivum (3IZR and others) was used to fit missing proteins form the two X-ray structures. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation |
Output model | PDB-4v8m: |
-Atomic model buiding 2
Initial model | PDB ID: 2xzm |
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Software | Name: Chimera |
Details | Protocol: Rigid body. The structure of the 80S from Yeast (3U5B and others) as well as the structure of the 60S from Tetrahymena thermophila (4A17 and others) were used as starting model for the 60S subunit model. The 40S from Tetrahymena thermophila (2XZM and 2XZN) as well as the 80S from Yeast were used as starting model for the 40S subunit model. The 80S model of Triticum aestivum (3IZR and others) was used to fit missing proteins form the two X-ray structures. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation |
Output model | PDB-4v8m: |
-Atomic model buiding 3
Initial model | PDB ID: 3izr |
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Software | Name: Chimera |
Details | Protocol: Rigid body. The structure of the 80S from Yeast (3U5B and others) as well as the structure of the 60S from Tetrahymena thermophila (4A17 and others) were used as starting model for the 60S subunit model. The 40S from Tetrahymena thermophila (2XZM and 2XZN) as well as the 80S from Yeast were used as starting model for the 40S subunit model. The 80S model of Triticum aestivum (3IZR and others) was used to fit missing proteins form the two X-ray structures. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation |
Output model | PDB-4v8m: |