[English] 日本語
Yorodumi- EMDB-3532: Cryo-EM reconstruction of the small subunit of the chloroplast ri... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3532 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM reconstruction of the small subunit of the chloroplast ribosome | |||||||||
Map data | Cryo-EM reconstruction of the 30S small subunit of the chloroplast ribosome | |||||||||
Sample |
| |||||||||
Keywords | chloroplast / translation / ribosome / cryo-EM | |||||||||
Function / homology | Function and homology information chloroplast rRNA processing / plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / mitochondrial translation / chloroplast thylakoid membrane / ribosomal small subunit binding ...chloroplast rRNA processing / plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / mitochondrial translation / chloroplast thylakoid membrane / ribosomal small subunit binding / chloroplast / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / mitochondrion / RNA binding / cytosol Similarity search - Function | |||||||||
Biological species | Spinacia oleracea (spinach) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Bieri P / Leibundgut M | |||||||||
Citation | Journal: EMBO J / Year: 2017 Title: The complete structure of the chloroplast 70S ribosome in complex with translation factor pY. Authors: Philipp Bieri / Marc Leibundgut / Martin Saurer / Daniel Boehringer / Nenad Ban / Abstract: Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, ...Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3532.map.gz | 9.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3532-v30.xml emd-3532.xml | 42.1 KB 42.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3532_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_3532.png | 139.1 KB | ||
Filedesc metadata | emd-3532.cif.gz | 10.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3532 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3532 | HTTPS FTP |
-Validation report
Summary document | emd_3532_validation.pdf.gz | 240.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3532_full_validation.pdf.gz | 239.4 KB | Display | |
Data in XML | emd_3532_validation.xml.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3532 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3532 | HTTPS FTP |
-Related structure data
Related structure data | 5mmjMC 3531C 3533C 5mmiC 5mmmC 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_3532.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM reconstruction of the 30S small subunit of the chloroplast ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Chloroplast 70S ribosome
+Supramolecule #1: Chloroplast 70S ribosome
+Macromolecule #1: 50S ribosomal protein L31
+Macromolecule #2: plastid ribosomal protein bS1c
+Macromolecule #4: 30S ribosomal protein S2, chloroplastic
+Macromolecule #5: 30S ribosomal protein S3, chloroplastic
+Macromolecule #6: 30S ribosomal protein S4, chloroplastic
+Macromolecule #7: 30S ribosomal protein S5, chloroplastic
+Macromolecule #8: plastid ribosomal protein bS6c
+Macromolecule #9: 30S ribosomal protein S7, chloroplastic
+Macromolecule #10: 30S ribosomal protein S8, chloroplastic
+Macromolecule #11: plastid ribosomal protein uS9c
+Macromolecule #12: plastid ribosomal protein uS10c
+Macromolecule #13: 30S ribosomal protein S11, chloroplastic
+Macromolecule #14: 30S ribosomal protein S12, chloroplastic
+Macromolecule #15: plastid ribosomal protein uS13c
+Macromolecule #16: 30S ribosomal protein S14, chloroplastic
+Macromolecule #17: 30S ribosomal protein S15, chloroplastic
+Macromolecule #18: 30S ribosomal protein S16, chloroplastic
+Macromolecule #19: plastid ribosomal protein uS17c
+Macromolecule #20: 30S ribosomal protein S18, chloroplastic
+Macromolecule #21: 30S ribosomal protein S19 alpha, chloroplastic
+Macromolecule #22: plastid ribosomal protein bS20c
+Macromolecule #23: plastid ribosomal protein bS21c
+Macromolecule #24: 30S ribosomal protein 2, chloroplastic
+Macromolecule #25: 30S ribosomal protein 3, chloroplastic
+Macromolecule #26: 30S ribosomal protein S31, chloroplastic
+Macromolecule #27: Ribosome-binding factor PSRP1, chloroplastic
+Macromolecule #3: 16S ribosomal RNA
+Macromolecule #28: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.12 mg/mL | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.6 Component:
| |||||||||||||||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 2-8 / Number real images: 2796 / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 111.6 |
---|---|
Output model | PDB-5mmj: |