+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10654 | |||||||||
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Title | Structure of the plant mitochondrial ribosome | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information 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 / valine catabolic process / aminoacyl-tRNA ligase activity / karyogamy / pollen development / : / regulation of programmed cell death / embryo development ending in seed dormancy / cell communication / Hydrolases; Acting on ester bonds; Thioester hydrolases / vacuole organization / nucleus localization / mitochondrial large ribosomal subunit / mitochondrial membrane organization / positive regulation of translational fidelity / mitochondrial small ribosomal subunit / vacuole / mitochondrial ribosome / plastid / mitochondrial translation / translation elongation factor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / aminopeptidase activity / ribosome assembly / response to cold / chloroplast / cytosolic ribosome / mRNA 5'-UTR binding / trans-Golgi network / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / regulation of gene expression / negative regulation of translation / rRNA binding / transcription cis-regulatory region binding / ribosome / endosome / mitochondrial matrix / structural constituent of ribosome / translation / copper ion binding / mRNA binding / Golgi apparatus / mitochondrion / RNA binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) / thale cress (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.86 Å | |||||||||
Authors | Soufari H / Waltz F / Giege P / Hashem Y | |||||||||
Funding support | France, 1 items
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Citation | 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10654.map.gz | 227.4 MB | EMDB map data format | |
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Header (meta data) | emd-10654-v30.xml emd-10654.xml | 99.3 KB 99.3 KB | Display Display | EMDB header |
Images | emd_10654.png | 152.9 KB | ||
Others | emd_10654_additional_1.map.gz emd_10654_additional_2.map.gz | 227.1 MB 225.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10654 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10654 | HTTPS FTP |
-Related structure data
Related structure data | 6xywMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10654.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 10654 additional 1.map
File | emd_10654_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 10654 additional 2.map
File | emd_10654_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : The large mitoribosomal subunit of the Plant mitoribosome
+Supramolecule #1: The large mitoribosomal subunit of the Plant mitoribosome
+Macromolecule #1: 60S ribosomal protein L2, mitochondrial
+Macromolecule #2: Expressed protein
+Macromolecule #3: 50S ribosomal protein L3-2, mitochondrial
+Macromolecule #4: Ribosomal protein L35
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 60S ribosomal protein L5, mitochondrial
+Macromolecule #7: Putative ribosomal protein L6
+Macromolecule #8: Ribosomal protein L9/RNase H1
+Macromolecule #9: At4g35490
+Macromolecule #10: At1g01640
+Macromolecule #11: 50S ribosomal protein HLP, mitochondrial
+Macromolecule #12: Ribosomal protein L18e/L15 superfamily protein
+Macromolecule #13: 60S ribosomal protein L16, mitochondrial
+Macromolecule #14: At5g09770
+Macromolecule #15: At5g27820
+Macromolecule #16: At1g24240/F3I6_17
+Macromolecule #17: 50S ribosomal protein L20
+Macromolecule #18: 50S ribosomal protein L21, mitochondrial
+Macromolecule #19: AT1G52370 protein
+Macromolecule #20: At4g39880
+Macromolecule #21: 50S ribosomal protein L24
+Macromolecule #22: Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding dom...
+Macromolecule #23: 50S ribosomal protein L27
+Macromolecule #24: AT4g31460/F3L17_30
+Macromolecule #25: At1g07830/F24B9_7
+Macromolecule #26: Ribosomal protein L31
+Macromolecule #27: At1g26740/T24P13_11
+Macromolecule #28: At3g06320
+Macromolecule #29: Ribosomal protein
+Macromolecule #30: At4g05400
+Macromolecule #31: At5g40080
+Macromolecule #32: Mitochondrial ribosomal protein L51/S25/CI-B8 family protein
+Macromolecule #33: At1g14620/T5E21_15
+Macromolecule #34: 39S ribosomal protein
+Macromolecule #35: At4g22000
+Macromolecule #36: Uncharacterized protein At1g27435/F17L21.30
+Macromolecule #37: At1g73940/F2P9_19
+Macromolecule #38: At3g51010
+Macromolecule #39: Pentatricopeptide repeat-containing protein At1g60770
+Macromolecule #40: rPPR*
+Macromolecule #41: Pentatricopeptide repeat-containing protein PNM1, mitochondrial
+Macromolecule #42: UNK-6
+Macromolecule #45: Ribosomal protein S3, mitochondrial
+Macromolecule #46: Ribosomal protein S7, mitochondrial
+Macromolecule #47: 30S ribosomal protein S9, mitochondrial
+Macromolecule #48: 40S ribosomal protein S10, mitochondrial
+Macromolecule #49: Small ribosomal subunit protein S13, mitochondrial
+Macromolecule #50: At2g34520
+Macromolecule #51: 40S ribosomal protein S19, mitochondrial
+Macromolecule #52: Mitochondrial 28S ribosomal protein S29-like protein
+Macromolecule #53: 37S ribosomal protein S27
+Macromolecule #54: AT3G18240 protein
+Macromolecule #55: CX9C domain-containing protein
+Macromolecule #56: 30S ribosomal protein S31, mitochondrial
+Macromolecule #57: Pentatricopeptide repeat-containing protein At3g02650, mitochondrial
+Macromolecule #58: UNK-5
+Macromolecule #59: mS31/mS46
+Macromolecule #60: Ribosomal protein S2, mitochondrial
+Macromolecule #61: Ribosomal protein S4, mitochondrial
+Macromolecule #62: At1g64880
+Macromolecule #63: Translation elongation factor EF1B/ribosomal protein S6 family protein
+Macromolecule #64: 40S ribosomal protein S15a-5
+Macromolecule #65: Probable ribosomal protein S11, mitochondrial
+Macromolecule #66: At1g15810/F7H2_23
+Macromolecule #67: 30S ribosomal protein S16-2, chloroplastic/mitochondrial
+Macromolecule #68: Nucleic acid-binding, OB-fold-like protein
+Macromolecule #69: F10K1.8 protein
+Macromolecule #70: Ribosomal protein S21 family protein
+Macromolecule #71: Uncharacterized protein
+Macromolecule #72: AT5g49210/K21P3_8
+Macromolecule #73: 28S ribosomal S34 protein
+Macromolecule #74: mS38
+Macromolecule #75: At5g26800
+Macromolecule #76: Gb
+Macromolecule #77: 3-hydroxyisobutyryl-CoA hydrolase-like protein 2, mitochondrial
+Macromolecule #78: rPPR*
+Macromolecule #79: rPPR*
+Macromolecule #80: Adenylyl cyclase
+Macromolecule #81: UNK-3
+Macromolecule #82: UNK-2
+Macromolecule #83: UNK-4
+Macromolecule #84: UNK-1
+Macromolecule #86: At5g55140
+Macromolecule #87: 50S ribosomal protein L10
+Macromolecule #88: rPPR*
+Macromolecule #89: Ribosomal protein S12, mitochondrial
+Macromolecule #43: RNA (2842-MER)
+Macromolecule #44: RNA (118-MER)
+Macromolecule #85: RNA (1743-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 3.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf (ver. 1.06) |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.7) |
Final 3D classification | Number classes: 10 / Avg.num./class: 15043 / Software - Name: RELION (ver. 3.0.7) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7) |
Final reconstruction | Number classes used: 4 / Resolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 65280 |