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Yorodumi- EMDB-17208: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RIBOSO... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17208 | |||||||||
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Title | CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RIBOSOME : PARENTAL STRAIN | |||||||||
Map data | 80S_composite_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 / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / regulation of cytokinesis / 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 / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / ribosome biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / regulation of cell population proliferation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / 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_17208.map.gz | 380.6 MB | EMDB map data format | |
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Header (meta data) | emd-17208-v30.xml emd-17208.xml | 109.2 KB 109.2 KB | Display Display | EMDB header |
Images | emd_17208.png | 99.5 KB | ||
Filedesc metadata | emd-17208.cif.gz | 20.8 KB | ||
Others | emd_17208_additional_1.map.gz emd_17208_half_map_1.map.gz emd_17208_half_map_2.map.gz | 337.7 MB 339.2 MB 339.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17208 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17208 | HTTPS FTP |
-Validation report
Summary document | emd_17208_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_17208_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_17208_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_17208_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17208 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17208 | 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_17208.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | 80S_composite_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
-Additional map: 80S consensus map
File | emd_17208_additional_1.map | ||||||||||||
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Annotation | 80S_consensus_map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map1 for 80S consensus map
File | emd_17208_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_17208_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 : CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RIBOSO...
+Supramolecule #1: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RIBOSO...
+Macromolecule #1: LSUa rRNA
+Macromolecule #2: SSU rRNA
+Macromolecule #3: LSUb rRNA
+Macromolecule #4: SrRNA-4
+Macromolecule #5: SrRNA-2
+Macromolecule #6: SrRNA-6
+Macromolecule #7: SrRNA-1
+Macromolecule #8: 5S rRNA
+Macromolecule #9: 5.8S rRNA
+Macromolecule #10: E-SITE TRNA
+Macromolecule #11: Ribosomal protein S10
+Macromolecule #12: uS14
+Macromolecule #13: Ubiquitin-60S ribosomal protein L40
+Macromolecule #14: RNA-binding protein
+Macromolecule #15: 40S ribosomal protein S14
+Macromolecule #16: 40S ribosomal protein S15, putative
+Macromolecule #17: 40S ribosomal protein S15a, putative
+Macromolecule #18: 40S ribosomal protein S16, putative
+Macromolecule #19: 40S ribosomal protein S18, putative
+Macromolecule #20: Ribosomal protein S19, putative
+Macromolecule #21: 40S ribosomal protein S2, putative
+Macromolecule #22: 40S ribosomal protein S21, putative
+Macromolecule #23: 40S ribosomal protein S23, putative
+Macromolecule #24: 40S ribosomal protein S24
+Macromolecule #25: 40S ribosomal protein S25
+Macromolecule #26: 40S ribosomal protein S26
+Macromolecule #27: 40S ribosomal protein S27, putative
+Macromolecule #28: 40S ribosomal protein S3, putative
+Macromolecule #29: 40S ribosomal protein S30
+Macromolecule #30: 40S ribosomal protein S33, putative
+Macromolecule #31: 40S ribosomal protein S17, putative
+Macromolecule #32: 40S ribosomal protein S3a
+Macromolecule #33: 40S ribosomal protein S4
+Macromolecule #34: 40S ribosomal protein S5, putative
+Macromolecule #35: 40S ribosomal protein S6
+Macromolecule #36: 40S ribosomal protein S7
+Macromolecule #37: 40S ribosomal protein S8
+Macromolecule #38: Probable 40S ribosomal protein S9
+Macromolecule #39: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #40: 40S ribosomal protein SA
+Macromolecule #41: 40S ribosomal protein S10, putative
+Macromolecule #42: 40S ribosomal proteins S11, putative
+Macromolecule #43: 40S ribosomal protein S13, putative
+Macromolecule #44: 60S ribosomal subunit protein L31, putative
+Macromolecule #45: 60S ribosomal protein L27
+Macromolecule #46: 60S ribosomal protein L27a
+Macromolecule #47: 60S ribosomal protein L28, putative
+Macromolecule #48: 60S ribosomal protein L29
+Macromolecule #49: 60S ribosomal protein L2, putative
+Macromolecule #50: Ribosomal protein L41
+Macromolecule #51: 60S ribosomal protein L30
+Macromolecule #52: Ribosomal protein L3, mitochondrial, putative
+Macromolecule #53: 60S ribosomal protein L18
+Macromolecule #54: 60S ribosomal protein L34, putative
+Macromolecule #55: 60S ribosomal protein L10, putative
+Macromolecule #56: 60S ribosomal protein L35, putative
+Macromolecule #57: 60S ribosomal protein L11, putative
+Macromolecule #58: 60S ribosomal protein L35A, putative
+Macromolecule #59: Ribosomal protein L36, putative
+Macromolecule #60: 60S ribosomal protein L13
+Macromolecule #61: Ribosomal protein L37
+Macromolecule #62: 60S ribosomal protein L13a, putative
+Macromolecule #63: 60S ribosomal protein L37a, putative
+Macromolecule #64: 60S ribosomal protein L38, putative
+Macromolecule #65: 60S ribosomal protein L39, putative
+Macromolecule #66: Ribosomal protein L15
+Macromolecule #67: 60S ribosomal protein L17, putative
+Macromolecule #68: 60S ribosomal protein L4
+Macromolecule #69: 60S ribosomal protein L18a
+Macromolecule #70: Ubiquitin-60S ribosomal protein L40
+Macromolecule #71: 60S ribosomal protein L19, putative
+Macromolecule #72: 60S ribosomal protein L44
+Macromolecule #73: 60S ribosomal protein L21E, putative
+Macromolecule #74: 60S ribosomal protein L5, putative
+Macromolecule #75: 60S ribosomal protein L22, putative
+Macromolecule #76: 60S ribosomal protein L6, putative
+Macromolecule #77: 60S ribosomal protein L23, putative
+Macromolecule #78: 60S ribosomal protein L23a
+Macromolecule #79: 60S ribosomal protein L7, putative
+Macromolecule #80: 60S ribosomal protein L7a
+Macromolecule #81: 60S ribosomal protein L24, putative
+Macromolecule #82: 60S ribosomal protein L9, putative
+Macromolecule #83: 60S ribosomal protein L26, putative
+Macromolecule #84: 60S ribosomal protein L32, putative
+Macromolecule #85: 40S ribosomal protein L14, putative
+Macromolecule #86: 40S ribosomal protein S12
+Macromolecule #87: MAGNESIUM ION
+Macromolecule #88: POTASSIUM ION
+Macromolecule #89: SODIUM ION
+Macromolecule #90: ZINC ION
+Macromolecule #91: water
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.17 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 |