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Open data
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Basic information
Entry | Database: PDB / ID: 6xyw | ||||||
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Title | Structure of the plant mitochondrial ribosome | ||||||
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![]() | RIBOSOME / Mitochondria / Plant | ||||||
Function / homology | ![]() embryo sac central cell differentiation / endosperm cellularization / gametophyte development / pollen tube development / polar nucleus fusion / regulation of starch biosynthetic process / pollen germination / endosperm development / double fertilization forming a zygote and endosperm / plastid translation ...embryo sac central cell differentiation / endosperm cellularization / gametophyte development / pollen tube development / polar nucleus fusion / regulation of starch biosynthetic process / pollen germination / endosperm development / double fertilization forming a zygote and endosperm / plastid translation / : / embryo sac development / 3-hydroxyisobutyryl-CoA hydrolase activity / aminoacyl-tRNA ligase activity / karyogamy / valine catabolic process / pollen development / regulation of programmed cell death / nucleus localization / embryo development ending in seed dormancy / cell communication / Hydrolases; Acting on ester bonds; Thioester hydrolases / vacuole organization / positive regulation of translational fidelity / mitochondrial large ribosomal subunit / mitochondrial membrane organization / mitochondrial small ribosomal subunit / vacuole / plastid / mitochondrial ribosome / mitochondrial translation / translation elongation factor activity / cytosolic ribosome / aminopeptidase activity / ribosome assembly / response to cold / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / trans-Golgi network / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / regulation of gene expression / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / negative regulation of translation / transcription cis-regulatory region binding / ribosome / endosome / structural constituent of ribosome / mitochondrial matrix / translation / copper ion binding / mRNA binding / Golgi apparatus / mitochondrion / RNA binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.86 Å | ||||||
![]() | Soufari, H. / Waltz, F. / Bochler, A. / Giege, P. / Hashem, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the RNA-rich plant mitochondrial ribosome. Authors: Florent Waltz / Heddy Soufari / Anthony Bochler / Philippe Giegé / Yaser Hashem / ![]() Abstract: The vast majority of eukaryotic cells contain mitochondria, essential powerhouses and metabolic hubs. These organelles have a bacterial origin and were acquired during an early endosymbiosis event. ...The vast majority of eukaryotic cells contain mitochondria, essential powerhouses and metabolic hubs. These organelles have a bacterial origin and were acquired during an early endosymbiosis event. Mitochondria possess specialized gene expression systems composed of various molecular machines, including the mitochondrial ribosomes (mitoribosomes). Mitoribosomes are in charge of translating the few essential mRNAs still encoded by mitochondrial genomes. While chloroplast ribosomes strongly resemble those of bacteria, mitoribosomes have diverged significantly during evolution and present strikingly different structures across eukaryotic species. In contrast to animals and trypanosomatids, plant mitoribosomes have unusually expanded ribosomal RNAs and have conserved the short 5S rRNA, which is usually missing in mitoribosomes. We have previously characterized the composition of the plant mitoribosome, revealing a dozen plant-specific proteins in addition to the common conserved mitoribosomal proteins. In spite of the tremendous recent advances in the field, plant mitoribosomes remained elusive to high-resolution structural investigations and the plant-specific ribosomal features of unknown structures. Here, we present a cryo-electron microscopy study of the plant 78S mitoribosome from cauliflower at near-atomic resolution. We show that most of the plant-specific ribosomal proteins are pentatricopeptide repeat proteins (PPRs) that deeply interact with the plant-specific rRNA expansion segments. These additional rRNA segments and proteins reshape the overall structure of the plant mitochondrial ribosome, and we discuss their involvement in the membrane association and mRNA recruitment prior to translation initiation. Finally, our structure unveils an rRNA-constructive phase of mitoribosome evolution across eukaryotes. | ||||||
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 | ![]() | 4.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 328.2 KB | Display | |
Data in CIF | ![]() | 577.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 10654MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
+60S ribosomal protein ... , 3 types, 3 molecules AaAeAm
+Protein , 49 types, 49 molecules AbAfAiAjAnAoApAsAtAxAyABACAEAFAGAIAJAKAMANAPBlBmBxBzBABPBFBd...
+50S ribosomal protein ... , 8 types, 8 molecules AcAdAkAqArAuAwAh
+Ribosomal protein ... , 11 types, 11 molecules ADAgAlAvAABbBfBaBcBsBk
+Mitochondrial ... , 2 types, 2 molecules AHBw
+Uncharacterized ... , 2 types, 2 molecules ALBu
+Pentatricopeptide repeat-containing protein ... , 3 types, 3 molecules AOAQBG
+Protein/peptide , 2 types, 2 molecules ARBO
+RNA chain , 3 types, 3 molecules 132
+30S ribosomal protein ... , 3 types, 3 molecules BhBtBo
+40S ribosomal protein ... , 3 types, 3 molecules BiBrBg
-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 large mitoribosomal subunit of the Plant mitoribosome Type: RIBOSOME Entity ID: #1, #10-#19, #2, #20-#29, #3, #30-#39, #4, #40-#49, #5, #50-#59, #6, #60-#69, #7, #70-#79, #8, #80-#89, #9 Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 30 µm |
Image recording | Average exposure time: 1 sec. / Electron dose: 3 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65280 / Num. of class averages: 4 / Symmetry type: POINT |