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Yorodumi- EMDB-56567: Structure of the Chlamydomonas reinhardtii chlororibosome with P-... -
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Open data
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Basic information
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| Title | Structure of the Chlamydomonas reinhardtii chlororibosome with P-site tRNA | |||||||||
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Keywords | chloroplast / ribosome / translation / chlororibosome | |||||||||
| Function / homology | Function and homology informationmitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / plastid / chloroplast / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit ...mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / plastid / chloroplast / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / mitochondrion / RNA binding / cytoplasm Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
Authors | Waltz F / Kater L / Engel BD | |||||||||
| Funding support | Switzerland, 2 items
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Citation | Journal: bioRxiv / Year: 2026Title: Chloroplast-encoded small subunit extensions reshape the Chlamydomonas chlororibosome. Authors: Florent Waltz / Philippe A Lehner / Philippe Van der Stappen / Lukas Kater / Stefan Pfeffer / Benjamin D Engel / ![]() Abstract: Chloroplast ribosomes (chlororibosomes) synthesize the core protein components of the photosynthetic apparatus, yet their structural diversity outside flowering plants remains largely unexplored. ...Chloroplast ribosomes (chlororibosomes) synthesize the core protein components of the photosynthetic apparatus, yet their structural diversity outside flowering plants remains largely unexplored. Here, we combine in situ cryo-electron tomography (cryo-ET) with single-particle cryo-electron microscopy (cryo-EM) to determine the structure of the chlororibosome from the unicellular green alga . Subtomogram averaging of chlororibosomes in their native environment, resolved to ~5 Å resolution and in distinct translational states, reveals particles both free in the stroma and loosely tethered to thylakoid membranes. These reconstructions uncover an additional "arm" domain on the small subunit. High-resolution single-particle reconstruction of isolated chlororibosomes to ~2.5 Å, in states bound either to the inhibitory translation factor pY or to a nascent chain-linked P-site tRNA, reveals that this domain is built primarily from extensive chloroplast-encoded insertions and extensions of conserved small subunit proteins, supported by chlororibosome-specific ribosomal proteins. The arm domain is located around the mRNA entry and exit channels, suggesting a role in stabilizing the mRNA trajectory through the small subunit and organizing chloroplast polysomes. Together, these data reveal unexpected structural variation of algal chlororibosomes and suggest that chloroplast translation has diversified substantially even among relatively closely related photosynthetic lineages. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_56567.map.gz | 13.4 MB | EMDB map data format | |
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| Header (meta data) | emd-56567-v30.xml emd-56567.xml | 73 KB 73 KB | Display Display | EMDB header |
| Images | emd_56567.png | 153.6 KB | ||
| Filedesc metadata | emd-56567.cif.gz | 17.8 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-56567 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-56567 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 28jwMC ![]() 28luC ![]() 9tvuC C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_56567.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.0631 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Chloroplast ribosome
+Supramolecule #1: Chloroplast ribosome
+Macromolecule #1: cL38/PSRP6
+Macromolecule #4: bL33c
+Macromolecule #5: bL34c
+Macromolecule #6: 50S ribosomal protein L35
+Macromolecule #7: Large ribosomal subunit protein bL36c
+Macromolecule #8: Large ribosomal subunit protein uL2c
+Macromolecule #9: Large ribosomal subunit protein uL3c
+Macromolecule #10: Large ribosomal subunit protein uL4c
+Macromolecule #11: Large ribosomal subunit protein uL5c
+Macromolecule #12: Plastid ribosomal protein L6
+Macromolecule #13: Large ribosomal subunit protein bL9c
+Macromolecule #14: uL10c
+Macromolecule #15: Large ribosomal subunit protein uL11c
+Macromolecule #16: uL13c
+Macromolecule #17: Large ribosomal subunit protein uL14c
+Macromolecule #18: uL15c
+Macromolecule #19: Large ribosomal subunit protein uL16c
+Macromolecule #20: Large ribosomal subunit protein bL17c
+Macromolecule #21: Large ribosomal subunit protein uL18c
+Macromolecule #22: bL19c
+Macromolecule #23: Large ribosomal subunit protein bL20c
+Macromolecule #24: bL21c
+Macromolecule #25: Large ribosomal subunit protein uL22c
+Macromolecule #26: uL23c,Large ribosomal subunit protein uL23c
+Macromolecule #27: KOW domain-containing protein
+Macromolecule #28: bL27c
+Macromolecule #29: Large ribosomal subunit protein bL28c
+Macromolecule #30: uL29c
+Macromolecule #31: bL32c
+Macromolecule #32: 50S ribosomal protein L31
+Macromolecule #37: Ribosomal protein S1 homologue
+Macromolecule #38: Small ribosomal subunit protein uS4c
+Macromolecule #39: bS6c
+Macromolecule #40: Small ribosomal subunit protein uS7c
+Macromolecule #41: Small ribosomal subunit protein uS8c
+Macromolecule #42: Small ribosomal subunit protein uS10 domain-containing protein
+Macromolecule #43: Small ribosomal subunit protein uS11c
+Macromolecule #44: Small ribosomal subunit protein uS12c
+Macromolecule #45: uS13c
+Macromolecule #46: Small ribosomal subunit protein uS14c
+Macromolecule #47: 30S ribosomal protein S15
+Macromolecule #48: 30S ribosomal protein S16, chloroplastic
+Macromolecule #49: Small ribosomal subunit protein uS17c
+Macromolecule #50: Small ribosomal subunit protein bS18c
+Macromolecule #51: Small ribosomal subunit protein uS19c
+Macromolecule #52: bS20c
+Macromolecule #53: bS21c
+Macromolecule #54: 30S ribosomal protein 3, chloroplastic
+Macromolecule #55: cS26/PSRP8
+Macromolecule #56: Plastid-specific ribosomal protein-7
+Macromolecule #58: Small ribosomal subunit protein uS2c
+Macromolecule #59: Small ribosomal subunit protein uS3c
+Macromolecule #60: uS5c
+Macromolecule #61: Small ribosomal subunit protein uS9c
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 3S rRNA
+Macromolecule #33: 23S rRNA
+Macromolecule #34: 7S RNA
+Macromolecule #35: P-site tRNA
+Macromolecule #36: Nascent peptide
+Macromolecule #57: 16S rRNA
+Macromolecule #62: mRNA
+Macromolecule #63: MAGNESIUM ION
+Macromolecule #64: POTASSIUM ION
+Macromolecule #65: CHLORAMPHENICOL
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 2.5 mg/mL |
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| Buffer | pH: 7.5 |
| Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000 |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Keywords
Authors
Switzerland, 2 items
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Processing
FIELD EMISSION GUN
