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Yorodumi- EMDB-17249: CRYO-EM CONSENSUS MAP OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RI... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17249 | |||||||||
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Title | CRYO-EM CONSENSUS MAP OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RIBOSOME : PARENTAL STRAIN | |||||||||
Map data | 80S_CONSENSUS_MAP | |||||||||
Sample |
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Keywords | CRYO-EM / TRYPANOSOMA BRUCEI / 80S RIBOSOME / RIBOSOME | |||||||||
Function / homology | Function and homology information organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / post-transcriptional regulation of gene expression / 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 ...organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / post-transcriptional regulation of gene expression / 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 / RNA processing / 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 / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of cytokinesis / maturation of SSU-rRNA / small-subunit processome / regulation of cell growth / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / regulation of cell population proliferation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / apoptotic process / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.47 Å | |||||||||
Authors | Rajan KS / Yonath A | |||||||||
Funding support | European Union, Israel, 2 items
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Citation | Journal: Nat Commun / Year: 2023 Title: A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei. Authors: K Shanmugha Rajan / Hava Madmoni / Anat Bashan / Masato Taoka / Saurav Aryal / Yuko Nobe / Tirza Doniger / Beathrice Galili Kostin / Amit Blumberg / Smadar Cohen-Chalamish / Schraga Schwartz ...Authors: K Shanmugha Rajan / Hava Madmoni / Anat Bashan / Masato Taoka / Saurav Aryal / Yuko Nobe / Tirza Doniger / Beathrice Galili Kostin / Amit Blumberg / Smadar Cohen-Chalamish / Schraga Schwartz / Andre Rivalta / Ella Zimmerman / Ron Unger / Toshiaki Isobe / Ada Yonath / Shulamit Michaeli / Abstract: Trypanosomes are protozoan parasites that cycle between insect and mammalian hosts and are the causative agent of sleeping sickness. Here, we describe the changes of pseudouridine (Ψ) modification ...Trypanosomes are protozoan parasites that cycle between insect and mammalian hosts and are the causative agent of sleeping sickness. Here, we describe the changes of pseudouridine (Ψ) modification on rRNA in the two life stages of the parasite using four different genome-wide approaches. CRISPR-Cas9 knock-outs of all four snoRNAs guiding Ψ on helix 69 (H69) of the large rRNA subunit were lethal. A single knock-out of a snoRNA guiding Ψ530 on H69 altered the composition of the 80S monosome. These changes specifically affected the translation of only a subset of proteins. This study correlates a single site Ψ modification with changes in ribosomal protein stoichiometry, supported by a high-resolution cryo-EM structure. We propose that alteration in rRNA modifications could generate ribosomes preferentially translating state-beneficial proteins. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17249.map.gz | 337.7 MB | EMDB map data format | |
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Header (meta data) | emd-17249-v30.xml emd-17249.xml | 25.5 KB 25.5 KB | Display Display | EMDB header |
Images | emd_17249.png | 99.5 KB | ||
Filedesc metadata | emd-17249.cif.gz | 4.4 KB | ||
Others | emd_17249_half_map_1.map.gz emd_17249_half_map_2.map.gz | 339.2 MB 339.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17249 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17249 | HTTPS FTP |
-Validation report
Summary document | emd_17249_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_17249_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_17249_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_17249_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17249 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17249 | HTTPS FTP |
-Related structure data
Related structure data | 8ovaMC 8oveC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17249.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | 80S_CONSENSUS_MAP | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: HALF MAP1 FOR 80S CONSENSUS MAP
File | emd_17249_half_map_1.map | ||||||||||||
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Annotation | HALF_MAP1_FOR_80S_CONSENSUS_MAP | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: HALF MAP2 FOR 80S CONSENSUS MAP
File | emd_17249_half_map_2.map | ||||||||||||
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Annotation | HALF_MAP2_FOR_80S_CONSENSUS_MAP | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 80S ribosome
Entire | Name: 80S ribosome |
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Components |
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-Supramolecule #1: 80S ribosome
Supramolecule | Name: 80S ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#86 |
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Source (natural) | Organism: Trypanosoma brucei brucei (eukaryote) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.16 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 459985 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |