[English] 日本語
Yorodumi- PDB-8apn: Structure of the mitochondrial ribosome from Polytomella magna wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8apn | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the mitochondrial ribosome from Polytomella magna with tRNA bound to the P site | ||||||
Components |
| ||||||
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: 3.1 Å | ||||||
Authors | Tobiasson, V. / Berzina, I. / Amunts, A. | ||||||
Funding support | Sweden, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8apn.cif.gz | 4.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8apn.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8apn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8apn_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8apn_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8apn_validation.xml.gz | 415.9 KB | Display | |
Data in CIF | 8apn_validation.cif.gz | 703 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/8apn ftp://data.pdbj.org/pub/pdb/validation_reports/ap/8apn | HTTPS FTP |
-Related structure data
Related structure data | 15576MC 8a22C 8apoC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 15 types, 15 molecules A1A2A3A4A5A6A7A8A9B1B2B3B4C1C3
#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 |
---|---|
#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: 66621.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#4: RNA chain | Mass: 23661.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#5: RNA chain | Mass: 43735.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#6: RNA chain | Mass: 35225.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#7: RNA chain | Mass: 171975.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#8: RNA chain | Mass: 112621.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#9: RNA chain | Mass: 22130.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#60: 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 |
#61: RNA chain | Mass: 67696.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#62: 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 |
#63: RNA chain | Mass: 108517.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#108: RNA chain | Mass: 23344.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#109: RNA chain | Mass: 1264.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
+Protein , 91 types, 91 molecules AaAbAcAdAeAfAhAiAjAkAlAmAnAoApAqArAsAtAuAvAwAxAyAzACAEAFAGAH...
-Protein/peptide , 15 types, 15 molecules AAABADXiBDYbUaUdUeUhUiUjUkUlUm
#35: Protein/peptide | Mass: 5921.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
---|---|
#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) |
#58: Protein/peptide | Mass: 2949.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#93: Protein/peptide | Mass: 4004.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#97: Protein/peptide | Mass: 5864.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#111: Protein/peptide | Mass: 2813.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#112: Protein/peptide | Mass: 3677.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#113: Protein/peptide | Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#116: Protein/peptide | Mass: 4103.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#117: Protein/peptide | Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#118: Protein/peptide | Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#119: Protein/peptide | Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#120: Protein/peptide | Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) |
#121: 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
#122: Chemical | ChemComp-MG / #123: Chemical | ChemComp-K / #124: Chemical | ChemComp-ZN / | #125: Chemical | ChemComp-ATP / | #126: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mitochondrial ribosome from Polytomella magna in complex with P-site tRNA as well as mRNA Type: RIBOSOME / Entity ID: #1-#121 / Source: NATURAL | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Polytomella magna (plant) | ||||||||||||||||||||
Buffer solution | pH: 7.45 | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | 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 |
---|---|
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 |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2999000 | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: OTHER / Num. of particles: 59000 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER |