- EMDB-10654: Structure of the plant mitochondrial ribosome -
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Basic information
Entry
Database: EMDB / ID: EMD-10654
Title
Structure of the plant mitochondrial ribosome
Map data
Sample
Complex: The large mitoribosomal subunit of the Plant mitoribosome
Protein or peptide: x 86 types
RNA: x 3 types
Keywords
Ribosome / Mitochondria / Plant
Function / homology
Function and homology information
embryo sac central cell differentiation / endosperm cellularization / gametophyte development / pollen tube development / endosperm development / polar nucleus fusion / regulation of starch biosynthetic process / pollen germination / double fertilization forming a zygote and endosperm / 3-hydroxyisobutyryl-CoA hydrolase activity ...embryo sac central cell differentiation / endosperm cellularization / gametophyte development / pollen tube development / endosperm development / polar nucleus fusion / regulation of starch biosynthetic process / pollen germination / double fertilization forming a zygote and endosperm / 3-hydroxyisobutyryl-CoA hydrolase activity / embryo sac development / nucleus localization / pollen development / karyogamy / regulation of programmed cell death / embryo development ending in seed dormancy / cell communication / Hydrolases; Acting on ester bonds; Thioester hydrolases / vacuole organization / plant-type vacuole / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial membrane organization / mitochondrial translation / plastid / translation elongation factor activity / aminopeptidase activity / cytosolic ribosome / response to cold / chloroplast / trans-Golgi network / regulation of translation / large ribosomal subunit / ribosomal small subunit biogenesis / regulation of gene expression / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / transcription cis-regulatory region binding / endosome / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / copper ion binding / ribonucleoprotein complex / mRNA binding / Golgi apparatus / mitochondrion / RNA binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function
Mitochondrial ribosomal protein S7, plants / Ribosomal protein S3, mitochondrial, plant / : / IMS import disulfide relay-system, CHCH-CHCH-like Cx9C / CHCH-CHCH-like Cx9C, IMS import disulfide relay-system, / : / : / 30S ribosomal protein S31, plant / Ribosomal protein S31e / : ...Mitochondrial ribosomal protein S7, plants / Ribosomal protein S3, mitochondrial, plant / : / IMS import disulfide relay-system, CHCH-CHCH-like Cx9C / CHCH-CHCH-like Cx9C, IMS import disulfide relay-system, / : / : / 30S ribosomal protein S31, plant / Ribosomal protein S31e / : / PPR repeat / Ribosomal protein MRP10, mitochondrial / Eukaryotic mitochondrial regulator protein / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Small ribosomal subunit protein mS41 SAM domain / PPR repeat family / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / IGR protein motif / IGR / Cysteine alpha-hairpin motif superfamily / Mitochondrial 28S ribosomal protein S34 / Mitochondrial 28S ribosomal protein S34 / : / Pentatricopeptide repeat domain / 39S ribosomal protein L40, mitochondrial / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Pentatricopeptide (PPR) repeat profile. / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Ribosomal protein L27/L41, mitochondrial / : / Mitochondrial ribosomal protein L27 / 39S ribosomal protein L46, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / 30S ribosomal protein / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / ClpP/crotonase-like domain superfamily / Ribosomal protein L11, bacterial-type / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / : / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / RNA recognition motif / RNA recognition motif / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Ribosomal protein S19, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L36 / Ribosomal protein L36 superfamily Similarity search - Domain/homology
Uncharacterized protein / Large ribosomal subunit protein mL43 / Ribosomal protein S21 family protein / Large ribosomal subunit protein mL101 (rPPR4) / At1g24240/F3I6_17 / At4g22000 / Small ribosomal subunit protein mS80 (rPPR6) / Small ribosomal subunit protein uS19m / Large ribosomal subunit protein uL5m / Small ribosomal subunit protein uS10m ...Uncharacterized protein / Large ribosomal subunit protein mL43 / Ribosomal protein S21 family protein / Large ribosomal subunit protein mL101 (rPPR4) / At1g24240/F3I6_17 / At4g22000 / Small ribosomal subunit protein mS80 (rPPR6) / Small ribosomal subunit protein uS19m / Large ribosomal subunit protein uL5m / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS7m / Large ribosomal subunit protein uL2mz, N-terminal part / Ribosomal protein L31 / IMS import disulfide relay-system CHCH-CHCH-like Cx9C domain-containing protein / Adenylyl cyclase / Small ribosomal subunit protein uS4m / Large ribosomal subunit protein uL22c / At1g64880 / At5g26800 / At1g01640 / Small ribosomal subunit protein mS33 / Small ribosomal subunit protein uS9m / At1g14620/T5E21_15 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein bL21m / Ribosomal protein L35 / 50S ribosomal protein L20 / At5g09770 / At5g27820 / Small ribosomal subunit protein mS47 / Large ribosomal subunit protein uL4m / Small ribosomal subunit protein uS11m / Large ribosomal subunit protein uL2my, C-terminal part / Ribosomal protein / Small ribosomal subunit protein mS29 / Large ribosomal subunit protein uL14mz / Large ribosomal subunit protein mL53 / Large ribosomal subunit protein bL32m / AT5g49210/K21P3_8 / Uncharacterized protein At1g27435/F17L21.30 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein uL16m / Small ribosomal subunit protein uS3m / At1g73940/F2P9_19 / Small ribosomal subunit protein uS13m / 28S ribosomal S34 protein / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain-containing protein / Ribosomal protein L18e/L15 superfamily protein / Small ribosomal subunit protein mL104 (rPPR9) / Small ribosomal subunit protein uS2m / 50S ribosomal protein L10 / AT3g18240 / Small ribosomal subunit protein bS18c / Small ribosomal subunit protein uS15c / Large ribosomal subunit protein uL3m / Translation elongation factor EF1B/ribosomal protein S6 family protein / 50S ribosomal protein L24 / Small ribosomal subunit protein bS16m/bS16c / At5g40080 / Small ribosomal subunit protein mS75 / Large ribosomal subunit protein bL9c / Small ribosomal subunit protein uS8my / At4g05400 / At3g51010 / Small ribosomal subunit protein bTHXm / Large ribosomal subunit protein uL23m / Small ribosomal subunit protein uS14m / 50S ribosomal protein L33, chloroplastic / AT4g31460/F3L17_30 / At4g35490 / Small ribosomal subunit protein uS17c / Putative ribosomal protein L6 / 50S ribosomal protein L27 Similarity search - Component
Biological species
Arabidopsis thaliana (thale cress)
Method
single particle reconstruction / cryo EM / Resolution: 3.86 Å
Journal: Nat Plants / Year: 2020 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
Deposition
Jan 31, 2020
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Header (metadata) release
Apr 15, 2020
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Map release
Apr 15, 2020
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Update
Nov 6, 2024
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Current status
Nov 6, 2024
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Macromolecule #63: Translation elongation factor EF1B/ribosomal protein S6 family protein
Macromolecule
Name: Translation elongation factor EF1B/ribosomal protein S6 family protein type: protein_or_peptide / ID: 63 / Number of copies: 1 / Enantiomer: LEVO
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