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Yorodumi- PDB-6z1p: Structure of the mitochondrial ribosome from Tetrahymena thermophila -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z1p | |||||||||
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Title | Structure of the mitochondrial ribosome from Tetrahymena thermophila | |||||||||
Components |
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Keywords | RIBOSOME / Mitochondrial ribosome / mitochondria / ciliate / tetrahymena | |||||||||
Function / homology | Function and homology information : / peptide-methionine (R)-S-oxide reductase activity / 3-hydroxyisobutyryl-CoA hydrolase activity / protein repair / : / signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / iron-sulfur cluster assembly / mitochondrial ribosome ...: / peptide-methionine (R)-S-oxide reductase activity / 3-hydroxyisobutyryl-CoA hydrolase activity / protein repair / : / signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / iron-sulfur cluster assembly / mitochondrial ribosome / mitochondrial translation / NAD+-protein poly-ADP-ribosyltransferase activity / isomerase activity / ferric iron binding / 2 iron, 2 sulfur cluster binding / large ribosomal subunit / small ribosomal subunit / double-stranded DNA binding / response to oxidative stress / nucleic acid binding / membrane => GO:0016020 / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / mitochondrion / RNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Tetrahymena thermophila (eukaryote) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Tobiasson, V. / Amunts, A. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Elife / Year: 2020 Title: Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation. Authors: Victor Tobiasson / Alexey Amunts / Abstract: To understand the steps involved in the evolution of translation, we used , a ciliate with high coding capacity of the mitochondrial genome, as the model organism and characterized its mitochondrial ...To understand the steps involved in the evolution of translation, we used , a ciliate with high coding capacity of the mitochondrial genome, as the model organism and characterized its mitochondrial ribosome (mitoribosome) using cryo-EM. The structure of the mitoribosome reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit, while the large subunit lacks 5S rRNA. The structure also shows that the small subunit head is constrained, tRNA binding sites are formed by mitochondria-specific protein elements, conserved protein bS1 is excluded, and bacterial RNA polymerase binding site is blocked. We provide evidence for anintrinsic protein targeting system through visualization of mitochondria-specific mL105 by the exit tunnel that would facilitate the recruitment of a nascent polypeptide. Functional protein uS3m is encoded by three complementary genes from the nucleus and mitochondrion, establishing a link between genetic drift and mitochondrial translation. Finally, we reannotated nine open reading frames in the mitochondrial genome that code for mitoribosomal proteins. | |||||||||
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 | 6z1p.cif.gz | 10.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6z1p.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6z1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/6z1p ftp://data.pdbj.org/pub/pdb/validation_reports/z1/6z1p | HTTPS FTP |
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-Related structure data
Related structure data | 11032MC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 4 types, 4 molecules AaAbBaBb
#1: RNA chain | Mass: 89365.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: GenBank: 15011465 |
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#2: RNA chain | Mass: 743593.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: GenBank: 15011465 |
#49: RNA chain | Mass: 62976.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: GenBank: 15011465 |
#50: RNA chain | Mass: 448294.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: GenBank: 15011465 |
-Ribosomal protein ... , 20 types, 20 molecules AcAkAlAnApAqArAwAxABAIAJBgBiBlBmBnBrBsBX
#3: Protein | Mass: 29974.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q951B6 |
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#11: Protein | Mass: 12385.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q24IM4 |
#12: Protein | Mass: 26227.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q24C33 |
#14: Protein | Mass: 17816.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: W7XH77 |
#16: Protein | Mass: 13612.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q950Y1 |
#17: Protein | Mass: 34669.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: I7MF78 |
#18: Protein | Mass: 17462.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q951A0 |
#23: Protein | Mass: 42829.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q23CT9 |
#24: Protein | Mass: 16210.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q22EY1 |
#28: Protein | Mass: 35041.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: I7LU83 |
#35: Protein | Mass: 18506.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: I7MG40 |
#36: Protein | Mass: 21158.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q22RG0 |
#55: Protein | Mass: 15971.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: I7MHS2 |
#57: Protein | Mass: 87307.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: I7M4A2 |
#60: Protein | Mass: 15296.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q951B3 |
#61: Protein | Mass: 33437.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q951B9 |
#62: Protein | Mass: 12311.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q951B0 |
#66: Protein | Mass: 63883.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q23K82 |
#67: Protein | Mass: 11624.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q951B7 |
#98: Protein | Mass: 18509.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q951B8 |
-50S ribosomal protein ... , 9 types, 9 molecules AdAeAoAsAuAvAyAAAE
#4: Protein | Mass: 49883.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q22HG3 |
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#5: Protein | Mass: 41992.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: I7MGP2 |
#15: Protein | Mass: 45100.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: W7X626 |
#19: Protein | Mass: 27705.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: A4VE95 |
#21: Protein | Mass: 20232.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q235I3 |
#22: Protein | Mass: 27633.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: I7LVD3 |
#25: Protein | Mass: 26654.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q24C34 |
#27: Protein | Mass: 27380.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: I7M068 |
#31: Protein | Mass: 7237.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q22L35 |
+Protein , 59 types, 59 molecules AfAgAhAiAjAmAtAzACAFAGAHAKALAMANAOAPAQARASATAUAVBcBdBeBhBjBk...
-Protein/peptide , 3 types, 3 molecules ADBCBF
#30: Protein/peptide | Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) |
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#77: Protein/peptide | Mass: 3166.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) |
#80: Protein/peptide | Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) |
-30S ribosomal protein ... , 4 types, 4 molecules BfBoBpBq
#54: Protein | Mass: 40865.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: I7M4M7 |
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#63: Protein | Mass: 23138.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: Q22WF3 |
#64: Protein | Mass: 52066.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: I7M3F6 |
#65: Protein | Mass: 21427.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) References: UniProt: I7M6C7 |
-Non-polymers , 4 types, 398 molecules
#100: Chemical | ChemComp-MG / #101: Chemical | #102: Chemical | #103: Chemical | ChemComp-ATP / | |
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-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: The mitochondrial ribosome from tetrahymena thermophila Type: RIBOSOME / Entity ID: #1-#99 / Source: NATURAL |
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Molecular weight | Value: 4.0 MDa / Experimental value: NO |
Source (natural) | Organism: Tetrahymena thermophila SB210 (eukaryote) |
Buffer solution | pH: 7.45 |
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 magnification: 92000 X / Calibrated defocus min: 200 nm / Calibrated defocus max: 3200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 6 sec. / Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 20 / Used frames/image: 2-20 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99300 / Symmetry type: POINT |