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Yorodumi- PDB-7aoi: Trypanosoma brucei mitochondrial ribosome large subunit assembly ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aoi | |||||||||||||||||||||
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Title | Trypanosoma brucei mitochondrial ribosome large subunit assembly intermediate | |||||||||||||||||||||
Components |
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Keywords | RIBOSOME / mitochondria / translation / trypanosoma / assembly / evolution / large subunit | |||||||||||||||||||||
Function / homology | Function and homology information pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / RNA methyltransferase activity / nuclear lumen / ciliary plasm / mitochondrial large ribosomal subunit / cyclosporin A binding / post-transcriptional regulation of gene expression / mitochondrial translation ...pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / RNA methyltransferase activity / nuclear lumen / ciliary plasm / mitochondrial large ribosomal subunit / cyclosporin A binding / post-transcriptional regulation of gene expression / mitochondrial translation / : / acyl binding / acyl carrier activity / RNA processing / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / lipid metabolic process / fatty acid biosynthetic process / large ribosomal subunit / protein folding / cytosolic large ribosomal subunit / RNA helicase activity / rRNA binding / hydrolase activity / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / mRNA binding / nucleolus / GTP binding / mitochondrion / RNA binding / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Trypanosoma brucei (eukaryote) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||||||||
Authors | Tobiasson, V. / Gahura, O. / Aibara, S. / Baradaran, R. / Zikova, A. / Amunts, A. | |||||||||||||||||||||
Funding support | Sweden, Czech Republic, 6items
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Citation | Journal: EMBO J / Year: 2021 Title: Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit. Authors: Victor Tobiasson / Ondřej Gahura / Shintaro Aibara / Rozbeh Baradaran / Alena Zíková / Alexey Amunts / Abstract: Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased ...Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased protein mass to provide insights into the biogenesis of the mitoribosomal large subunit. Structural characterization of a stable assembly intermediate revealed 22 assembly factors, some of which have orthologues/counterparts/homologues in mammalian genomes. These assembly factors form a protein network that spans a distance of 180 Å, shielding the ribosomal RNA surface. The central protuberance and L7/L12 stalk are not assembled entirely and require removal of assembly factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt-EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl-carrier protein plays a role in docking the L1 stalk, which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly while the exit tunnel is blocked. Together, this extensive network of accessory factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7aoi.cif.gz | 3.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7aoi.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7aoi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aoi_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7aoi_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7aoi_validation.xml.gz | 393.5 KB | Display | |
Data in CIF | 7aoi_validation.cif.gz | 652 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/7aoi ftp://data.pdbj.org/pub/pdb/validation_reports/ao/7aoi | HTTPS FTP |
-Related structure data
Related structure data | 11845MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 58 types, 59 molecules A1A2A3A5A8AIAPATAUAYAeAfAlAoApAtAvBABBBDBEBFBHBJBKBLBNBOBRBS...
-RNA chain , 1 types, 1 molecules AA
#6: RNA chain | Mass: 242538.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) |
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-Ribosomal protein ... , 6 types, 6 molecules AEAFAKAVAWAX
#7: Protein | Mass: 42538.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q580R4 |
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#8: Protein | Mass: 51178.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KTM7 |
#10: Protein | Mass: 29590.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LEQ0 |
#16: Protein | Mass: 20182.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LA68 |
#17: Protein | Mass: 31952.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L4Z4 |
#18: Protein | Mass: 19685.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KW11 |
-50S ribosomal protein ... , 3 types, 3 molecules ANARXG
#11: Protein | Mass: 20327.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LAE5 |
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#13: Protein | Mass: 30480.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LAG5 |
#70: Protein | Mass: 19559.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LE16 |
-Mitochondrial ... , 2 types, 2 molecules AgBI
#22: Protein | Mass: 22110.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LCE5 |
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#34: Protein | Mass: 37503.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KZH2 |
-Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules BQBZ
#40: Protein | Mass: 20286.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57WF8, peptidylprolyl isomerase |
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#47: Protein | Mass: 20411.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KTB1, peptidylprolyl isomerase |
-Protein/peptide , 10 types, 10 molecules UAUBUCUDUEUGUHUIUJUK
#54: Protein/peptide | Mass: 3287.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) |
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#55: Protein/peptide | Mass: 657.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) |
#56: Protein/peptide | Mass: 1013.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) |
#57: Protein/peptide | Mass: 586.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) |
#58: Protein/peptide | Mass: 870.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) |
#60: Protein/peptide | Mass: 1368.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) |
#61: Protein/peptide | Mass: 1226.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) |
#62: Protein/peptide | Mass: 2790.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) |
#63: Protein/peptide | Mass: 1794.960 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) |
#64: Protein/peptide | Mass: 3358.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) |
-Non-polymers , 6 types, 10 molecules
#83: Chemical | ChemComp-FES / | ||||||
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#84: Chemical | ChemComp-NAD / | ||||||
#85: Chemical | ChemComp-ZN / #86: Chemical | ChemComp-MG / | #87: Chemical | ChemComp-ADP / | #88: Chemical | |
-Details
Has ligand of interest | N |
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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: Trypanosoma brucei mitochondrial ribosome large subunit assembly intermediate Type: RIBOSOME / Entity ID: #1-#82 / Source: NATURAL |
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Molecular weight | Value: 2.23 MDa / Experimental value: YES |
Source (natural) | Organism: Trypanosoma brucei (eukaryote) / Cellular location: Mitochondrial Matrix / Organelle: Mitochondrion |
Buffer solution | pH: 7.45 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % |
-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 |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32300 / Symmetry type: POINT |
Atomic model building | Protocol: FLEXIBLE FIT |