+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13480 | |||||||||||||||
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Title | Large subunit of the Chlamydomonas reinhardtii mitoribosome | |||||||||||||||
Map data | Large subunit of the Chlamydomonas mitoribosome | |||||||||||||||
Sample |
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Function / homology | Function and homology information chloroplast rRNA processing / regulation of mitochondrial mRNA stability / ribonucleoprotein granule / mitochondrial RNA processing / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / ribosome assembly / chloroplast / ribosomal large subunit assembly ...chloroplast rRNA processing / regulation of mitochondrial mRNA stability / ribonucleoprotein granule / mitochondrial RNA processing / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / ribosome assembly / chloroplast / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / translation / mRNA binding / mitochondrion / RNA binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||
Authors | Waltz F / Soufari H / Hashem Y | |||||||||||||||
Funding support | European Union, France, 4 items
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Citation | Journal: Nat Commun / Year: 2021 Title: How to build a ribosome from RNA fragments in Chlamydomonas mitochondria. Authors: Florent Waltz / Thalia Salinas-Giegé / Robert Englmeier / Herrade Meichel / Heddy Soufari / Lauriane Kuhn / Stefan Pfeffer / Friedrich Förster / Benjamin D Engel / Philippe Giegé / ...Authors: Florent Waltz / Thalia Salinas-Giegé / Robert Englmeier / Herrade Meichel / Heddy Soufari / Lauriane Kuhn / Stefan Pfeffer / Friedrich Förster / Benjamin D Engel / Philippe Giegé / Laurence Drouard / Yaser Hashem / Abstract: Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the ...Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the few essential messenger RNAs still encoded by mitochondrial genomes. Here, we present a biochemical and structural characterization of the mitoribosome in the model green alga Chlamydomonas reinhardtii, as well as a functional study of some of its specific components. Single particle cryo-electron microscopy resolves how the Chlamydomonas mitoribosome is assembled from 13 rRNA fragments encoded by separate non-contiguous gene pieces. Additional proteins, mainly OPR, PPR and mTERF helical repeat proteins, are found in Chlamydomonas mitoribosome, revealing the structure of an OPR protein in complex with its RNA binding partner. Targeted amiRNA silencing indicates that these ribosomal proteins are required for mitoribosome integrity. Finally, we use cryo-electron tomography to show that Chlamydomonas mitoribosomes are attached to the inner mitochondrial membrane via two contact points mediated by Chlamydomonas-specific proteins. Our study expands our understanding of mitoribosome diversity and the various strategies these specialized molecular machines adopt for membrane tethering. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13480.map.gz | 394.4 MB | EMDB map data format | |
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Header (meta data) | emd-13480-v30.xml emd-13480.xml | 77.1 KB 77.1 KB | Display Display | EMDB header |
Images | emd_13480.png | 65.7 KB | ||
Others | emd_13480_half_map_1.map.gz emd_13480_half_map_2.map.gz | 339.9 MB 340.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13480 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13480 | HTTPS FTP |
-Related structure data
Related structure data | 7pktMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13480.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Large subunit of the Chlamydomonas mitoribosome | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.9 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_13480_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13480_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Large subunit of the mitochondrial ribosome of Chlamydomonas rein...
+Supramolecule #1: Large subunit of the mitochondrial ribosome of Chlamydomonas rein...
+Macromolecule #1: Ribosomal_L2_C domain-containing protein
+Macromolecule #2: uL3m
+Macromolecule #3: uL4m
+Macromolecule #4: uL5m
+Macromolecule #5: 50S ribosomal protein L9, chloroplastic
+Macromolecule #6: Mitochondrial ribosomal protein L13
+Macromolecule #7: uL14m
+Macromolecule #8: Ribosomal_L18e/L15P domain-containing protein
+Macromolecule #9: Ribosomal_L16 domain-containing protein
+Macromolecule #10: Mitochondrial ribosomal protein L17,bL17m
+Macromolecule #11: Mitochondrial ribosomal protein L19
+Macromolecule #12: 50S ribosomal protein L20
+Macromolecule #13: bL21m
+Macromolecule #14: uL22m
+Macromolecule #15: Mitochondrial ribosomal protein L23
+Macromolecule #16: KOW domain-containing protein,uL24m
+Macromolecule #17: Ribosomal_TL5_C domain-containing protein
+Macromolecule #18: bL27m
+Macromolecule #19: bL28m
+Macromolecule #20: uL29m
+Macromolecule #21: Ribosomal_L30 domain-containing protein
+Macromolecule #22: bL32m
+Macromolecule #23: Mitochondrial ribosomal protein L33
+Macromolecule #24: bL34m
+Macromolecule #25: bL35m
+Macromolecule #26: Plastid ribosomal protein L6
+Macromolecule #27: mL40
+Macromolecule #28: mL41
+Macromolecule #29: mL43
+Macromolecule #30: Mitochondrial ribosomal protein L17
+Macromolecule #31: mL63/57/60
+Macromolecule #32: mL59/64
+Macromolecule #33: mL80
+Macromolecule #34: mL87
+Macromolecule #35: bL36m
+Macromolecule #36: mL113
+Macromolecule #37: mL114
+Macromolecule #38: mL115
+Macromolecule #39: mL116
+Macromolecule #40: mL117
+Macromolecule #41: mL118
+Macromolecule #42: mL119
+Macromolecule #43: Unk1
+Macromolecule #44: PPR*
+Macromolecule #45: Unk2
+Macromolecule #46: L1 rRNA
+Macromolecule #47: L2a rRNA
+Macromolecule #48: L3a rRNA (5S)
+Macromolecule #49: L3b rRNA
+Macromolecule #50: L4 rRNA
+Macromolecule #51: L5 rRNA
+Macromolecule #52: L6 rRNA
+Macromolecule #53: L7 rRNA
+Macromolecule #54: L8 rRNA
+Macromolecule #55: ZINC ION
+Macromolecule #56: MAGNESIUM ION
+Macromolecule #57: FE2/S2 (INORGANIC) CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.6 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / 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 | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Average electron dose: 45.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: RANDOM ASSIGNMENT |
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Final 3D classification | Number classes: 6 / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Number classes used: 2 / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 101291 |