+Open data
-Basic information
Entry | Database: PDB / ID: 8a22 | ||||||
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Title | Structure of the mitochondrial ribosome from Polytomella magna | ||||||
Components |
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Keywords | RIBOSOME / mitoribosome / mitochondria / polytomella / fragmentation / rrna / evolution / translation | ||||||
Function / homology | ADENOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Biological species | Polytomella magna (plant) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å | ||||||
Authors | Tobiasson, V. / Berzina, I. / Amunts, A. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements. Authors: Victor Tobiasson / Ieva Berzina / Alexey Amunts / Abstract: Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 Å ...Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 Å resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway. Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3' rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a22.cif.gz | 4.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8a22.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8a22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a22_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8a22_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8a22_validation.xml.gz | 419 KB | Display | |
Data in CIF | 8a22_validation.cif.gz | 714.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/8a22 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/8a22 | HTTPS FTP |
-Related structure data
Related structure data | 15100MC 8apnC 8apoC 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 , 13 types, 13 molecules A1A2A3A4A5A6A7A8A9B1B2B3B4
#1: RNA chain | Mass: 35302.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616 |
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#2: RNA chain | Mass: 26056.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616 |
#3: RNA chain | Mass: 67578.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616 |
#4: RNA chain | Mass: 23661.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616 |
#5: RNA chain | Mass: 45703.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616 |
#6: RNA chain | Mass: 42369.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616 |
#7: RNA chain | Mass: 185617.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616 |
#8: RNA chain | Mass: 112621.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616 |
#9: RNA chain | Mass: 22130.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#58: RNA chain | Mass: 32708.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616 |
#59: RNA chain | Mass: 68920.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616 |
#60: RNA chain | Mass: 122239.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616 |
#61: RNA chain | Mass: 112061.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616 |
+Protein , 89 types, 91 molecules AaAbAcAdAeAfAhAiAjAkAlAmAnAoApAqArAsAtAuAvAwAxAyAzACAEAFAGAH...
-Protein/peptide , 15 types, 15 molecules AAABADXiBCYbUaUdUeUhUiUjUkUlUm
#35: Protein/peptide | Mass: 5921.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
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#36: Protein/peptide | Mass: 6149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#38: Protein/peptide | Mass: 5495.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#56: Protein/peptide | Mass: 2949.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#90: Protein/peptide | Mass: 4004.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#95: Protein/peptide | Mass: 5864.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#106: Protein/peptide | Mass: 2813.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#108: Protein/peptide | Mass: 3677.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#109: Protein/peptide | Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#112: Protein/peptide | Mass: 4103.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#113: Protein/peptide | Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#114: Protein/peptide | Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#115: Protein/peptide | Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#116: Protein/peptide | Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#117: Protein/peptide | Mass: 954.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
-Non-polymers , 5 types, 649 molecules
#118: Chemical | ChemComp-MG / #119: Chemical | ChemComp-K / #120: Chemical | ChemComp-ZN / | #121: Chemical | ChemComp-ATP / | #122: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-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: Mitochondrial ribosome from Polytomella magna / Type: RIBOSOME / Entity ID: #1-#117 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Polytomella magna (plant) | ||||||||||||||||||||
Buffer solution | pH: 7.45 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-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 magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / C2 aperture diameter: 150 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 45850 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2999000 | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 184300 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER |