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- PDB-6z1p: Structure of the mitochondrial ribosome from Tetrahymena thermophila -
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Open data
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Basic information
Entry | Database: PDB / ID: 6z1p | |||||||||
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Title | Structure of the mitochondrial ribosome from Tetrahymena thermophila | |||||||||
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![]() | RIBOSOME / Mitochondrial ribosome / mitochondria / ciliate / tetrahymena | |||||||||
Function / homology | ![]() : / 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 / ferric iron binding / isomerase activity / 2 iron, 2 sulfur cluster binding / large ribosomal subunit / double-stranded DNA binding / small ribosomal subunit / nucleic acid binding / response to oxidative stress / membrane => GO:0016020 / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / mitochondrion / RNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Tobiasson, V. / Amunts, A. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 10.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 985.4 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 414.1 KB | Display | |
Data in CIF | ![]() | 722.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11032MC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() 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) ![]() References: GenBank: 15011465 |
#49: RNA chain | Mass: 62976.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 15011465 |
#50: RNA chain | Mass: 448294.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() 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) ![]() 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) ![]() References: UniProt: Q24IM4 |
#12: Protein | Mass: 26227.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q24C33 |
#14: Protein | Mass: 17816.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: W7XH77 |
#16: Protein | Mass: 13612.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q950Y1 |
#17: Protein | Mass: 34669.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: I7MF78 |
#18: Protein | Mass: 17462.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q951A0 |
#23: Protein | Mass: 42829.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q23CT9 |
#24: Protein | Mass: 16210.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q22EY1 |
#28: Protein | Mass: 35041.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: I7LU83 |
#35: Protein | Mass: 18506.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: I7MG40 |
#36: Protein | Mass: 21158.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q22RG0 |
#55: Protein | Mass: 15971.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: I7MHS2 |
#57: Protein | Mass: 87307.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: I7M4A2 |
#60: Protein | Mass: 15296.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q951B3 |
#61: Protein | Mass: 33437.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q951B9 |
#62: Protein | Mass: 12311.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q951B0 |
#66: Protein | Mass: 63883.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q23K82 |
#67: Protein | Mass: 11624.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q951B7 |
#98: Protein | Mass: 18509.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() 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) ![]() 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) ![]() References: UniProt: I7MGP2 |
#15: Protein | Mass: 45100.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: W7X626 |
#19: Protein | Mass: 27705.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A4VE95 |
#21: Protein | Mass: 20232.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q235I3 |
#22: Protein | Mass: 27633.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: I7LVD3 |
#25: Protein | Mass: 26654.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q24C34 |
#27: Protein | Mass: 27380.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: I7M068 |
#31: Protein | Mass: 7237.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() 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) ![]() |
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#77: Protein/peptide | Mass: 3166.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
#80: Protein/peptide | Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
-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) ![]() 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) ![]() References: UniProt: Q22WF3 |
#64: Protein | Mass: 52066.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: I7M3F6 |
#65: Protein | Mass: 21427.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: I7M6C7 |
-Non-polymers , 4 types, 398 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
#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 |
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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: ![]() |
Buffer solution | pH: 7.45 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |
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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 |