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Yorodumi- PDB-8ova: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RIBOSO... -
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-Basic information
Entry | Database: PDB / ID: 8ova | |||||||||
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Title | CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RIBOSOME : PARENTAL STRAIN | |||||||||
Components |
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Keywords | RIBOSOME / CRYO-EM / TRYPANOSOMA BRUCEI / 80S 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 / translation regulator activity / RNA processing / 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 / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of cytokinesis / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / regulation of cell growth / protein kinase C binding / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / regulation of cell population proliferation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 Å | |||||||||
Authors | Rajan, K.S. / Yonath, A. | |||||||||
Funding support | European Union, Israel, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ova.cif.gz | 5.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8ova.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ova.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/8ova ftp://data.pdbj.org/pub/pdb/validation_reports/ov/8ova | HTTPS FTP |
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-Related structure data
Related structure data | 17208MC 17249MC 17250MC 8oveC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 10 types, 10 molecules BAAABBBHBGBFBEBDBCAB
#1: RNA chain | Mass: 619662.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) |
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#2: RNA chain | Mass: 734961.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) |
#3: RNA chain | Mass: 494694.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) |
#4: RNA chain | Mass: 43694.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 10519 |
#5: RNA chain | Mass: 59196.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 10528 |
#6: RNA chain | Mass: 24646.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 62359081 |
#7: RNA chain | Mass: 69132.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 10528 |
#8: RNA chain | Mass: 38316.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 162230 |
#9: RNA chain | Mass: 67019.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 10527 |
#10: RNA chain | Mass: 6106.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) |
-Ribosomal protein ... , 7 types, 7 molecules AQAOBzBfBmBnBQ
#11: Protein | Mass: 13377.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) |
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#20: Protein | Mass: 18891.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q583K7 |
#50: Protein/peptide | Mass: 4348.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) |
#52: Protein | Mass: 48802.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q581Q1 |
#59: Protein | Mass: 12491.966 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CY6 |
#61: Protein | Mass: 10128.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q386L1 |
#66: Protein | Mass: 26461.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CY7 |
-Protein , 6 types, 6 molecules A8AzA6A7AEBh
#12: Protein | Mass: 6744.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) |
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#14: Protein | Mass: 30340.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q382D5 |
#38: Protein | Mass: 22098.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P17959 |
#39: Protein | Mass: 34727.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P69103 |
#42: Protein | Mass: 20132.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38CI4 |
#44: Protein | Mass: 21752.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38DH8 |
-Ubiquitin-60S ribosomal protein ... , 2 types, 2 molecules A9Bs
#13: Protein | Mass: 16936.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57WI3 |
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#70: Protein | Mass: 14685.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P21899 |
+40S ribosomal protein ... , 27 types, 27 molecules AHAIAJAKAMAPARASATAUAVAWAXAYAZALA0A1A2A3A4A5ACADAGBPAF
+60S ribosomal protein ... , 34 types, 34 molecules BaBbBcBdBeBgBIBjBKBkBLBlBNBOBoBpBqBRBrBSBTBtBUBuBVBvBWBXBwBx...
-Non-polymers , 5 types, 514 molecules
#87: Chemical | ChemComp-MG / #88: Chemical | ChemComp-K / #89: Chemical | ChemComp-NA / #90: Chemical | ChemComp-ZN / #91: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI PROCYCLIC FORM 80S RIBOSOME : PARENTAL STRAIN Type: RIBOSOME / Entity ID: #1-#86 / Source: NATURAL |
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Source (natural) | Organism: Trypanosoma brucei brucei (eukaryote) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 1.17 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459985 / Symmetry type: POINT | ||||||||||||||||||||||||
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