+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9572 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the large subunit of the chloro-ribosome | |||||||||
Map data | Chloro-ribosome LSU (50S) | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information plastid translation / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast / DNA-templated transcription termination / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...plastid translation / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast / DNA-templated transcription termination / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding Similarity search - Function | |||||||||
Biological species | Spinacia oleracea (spinach) / Spinach (spinach) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Ahmed T / Yin Z / Bhushan S | |||||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Cryo-EM structure of the large subunit of the spinach chloroplast ribosome. Authors: Tofayel Ahmed / Zhan Yin / Shashi Bhushan / Abstract: Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ...Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ribosome but certain differences are evident. The chloro-ribosome proteins are generally larger because of the presence of chloroplast-specific extensions in their N- and C-termini. The chloro-ribosome harbours six plastid-specific ribosomal proteins (PSRPs); four in the small subunit and two in the large subunit. Deletions and insertions occur throughout the rRNA sequence of the chloro-ribosome (except for the conserved peptidyl transferase center region) but the overall length of the rRNAs do not change significantly, compared to the E. coli. Although, recent advancements in cryo-electron microscopy (cryo-EM) have provided detailed high-resolution structures of ribosomes from many different sources, a high-resolution structure of the chloro-ribosome is still lacking. Here, we present a cryo-EM structure of the large subunit of the chloro-ribosome from spinach (Spinacia oleracea) at an average resolution of 3.5 Å. High-resolution map enabled us to localize and model chloro-ribosome proteins, chloroplast-specific protein extensions, two PSRPs (PSRP5 and 6) and three rRNA molecules present in the chloro-ribosome. Although comparable to E. coli, the polypeptide tunnel and the tunnel exit site show chloroplast-specific features. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9572.map.gz | 11.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-9572-v30.xml emd-9572.xml | 42.5 KB 42.5 KB | Display Display | EMDB header |
Images | emd_9572.png | 63.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9572 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9572 | HTTPS FTP |
-Related structure data
Related structure data | 5h1sMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_9572.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Chloro-ribosome LSU (50S) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Chloro-ribosome 50S
+Supramolecule #1: Chloro-ribosome 50S
+Macromolecule #1: 23S rRNA
+Macromolecule #2: Spinach chloroplast 4.5S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: 50S ribosomal protein L13, chloroplastic
+Macromolecule #5: 50S ribosomal protein L14, chloroplastic
+Macromolecule #6: 50S ribosomal protein L15
+Macromolecule #7: 50S ribosomal protein L16, chloroplastic
+Macromolecule #8: 50S ribosomal protein L17
+Macromolecule #9: 50S ribosomal protein L18
+Macromolecule #10: 50S ribosomal protein L19, chloroplastic
+Macromolecule #11: 50S ribosomal protein L20, chloroplastic
+Macromolecule #12: 50S ribosomal protein L21, chloroplastic
+Macromolecule #13: 50S ribosomal protein L22, chloroplastic
+Macromolecule #14: 50S ribosomal protein L23, chloroplastic
+Macromolecule #15: 50S ribosomal protein L24, chloroplastic
+Macromolecule #16: 50S ribosomal protein L27
+Macromolecule #17: 50S ribosomal protein L28
+Macromolecule #18: 50S ribosomal protein L29
+Macromolecule #19: 50S ribosomal protein L2, chloroplastic
+Macromolecule #20: 50S ribosomal protein L32, chloroplastic
+Macromolecule #21: 50S ribosomal protein L33, chloroplastic
+Macromolecule #22: 50S ribosomal protein L34, chloroplastic
+Macromolecule #23: 50S ribosomal protein L35, chloroplastic
+Macromolecule #24: 50S ribosomal protein L36, chloroplastic
+Macromolecule #25: 50S ribosomal protein L3
+Macromolecule #26: 50S ribosomal protein L4, chloroplastic
+Macromolecule #27: 50S ribosomal protein L5, chloroplastic
+Macromolecule #28: 50S ribosomal protein L6
+Macromolecule #29: 50S ribosomal protein L9
+Macromolecule #30: 50S ribosomal protein 5 alpha, chloroplastic
+Macromolecule #31: 50S ribosomal protein L31
+Macromolecule #32: 50S ribosomal protein 6, chloroplastic
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Details: 20 mM Tris HCl, pH 7.6, 100 mM KCl, 10 mM MgOAc, 100 mM sucrose, 7 mM 2-mercaptoethanol, 1 unit/ml RNase inhibitor, 0.1% protease inhibitor |
---|---|
Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.2 µm / Calibrated magnification: 109375 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 78000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Number real images: 1590 / Average electron dose: 26.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 338305 |
---|---|
CTF correction | Software - Name: CTFFIND3 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final 3D classification | Number classes: 200 / Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final reconstruction | Number classes used: 20 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 174949 |