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- EMDB-1417: Cryo-EM study of the Spinach chloroplast ribosome reveals the str... -
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Basic information
Entry | Database: EMDB / ID: EMD-1417 | |||||||||
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Title | Cryo-EM study of the Spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins | |||||||||
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![]() | Spinacea oleracea chloroplast 70S ribosome: ribosome-eukaryote | |||||||||
Function / homology | ![]() plastid small ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / cytosolic ribosome / mitochondrial large ribosomal subunit / maturation of LSU-rRNA / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Sharma MR / Wilson DN / Datta PP / Barat C / Schluenzen F / Fucini P / Agrawal RK | |||||||||
![]() | ![]() Title: Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins. Authors: Manjuli R Sharma / Daniel N Wilson / Partha P Datta / Chandana Barat / Frank Schluenzen / Paola Fucini / Rajendra K Agrawal / ![]() Abstract: Protein synthesis in the chloroplast is carried out by chloroplast ribosomes (chloro-ribosome) and regulated in a light-dependent manner. Chloroplast or plastid ribosomal proteins (PRPs) generally ...Protein synthesis in the chloroplast is carried out by chloroplast ribosomes (chloro-ribosome) and regulated in a light-dependent manner. Chloroplast or plastid ribosomal proteins (PRPs) generally are larger than their bacterial counterparts, and chloro-ribosomes contain additional plastid-specific ribosomal proteins (PSRPs); however, it is unclear to what extent these proteins play structural or regulatory roles during translation. We have obtained a three-dimensional cryo-EM map of the spinach 70S chloro-ribosome, revealing the overall structural organization to be similar to bacterial ribosomes. Fitting of the conserved portions of the x-ray crystallographic structure of the bacterial 70S ribosome into our cryo-EM map of the chloro-ribosome reveals the positions of PRP extensions and the locations of the PSRPs. Surprisingly, PSRP1 binds in the decoding region of the small (30S) ribosomal subunit, in a manner that would preclude the binding of messenger and transfer RNAs to the ribosome, suggesting that PSRP1 is a translation factor rather than a ribosomal protein. PSRP2 and PSRP3 appear to structurally compensate for missing segments of the 16S rRNA within the 30S subunit, whereas PSRP4 occupies a position buried within the head of the 30S subunit. One of the two PSRPs in the large (50S) ribosomal subunit lies near the tRNA exit site. Furthermore, we find a mass of density corresponding to chloro-ribosome recycling factor; domain II of this factor appears to interact with the flexible C-terminal domain of PSRP1. Our study provides evolutionary insights into the structural and functional roles that the PSRPs play during protein synthesis in chloroplasts. | |||||||||
Validation Report | ![]() ![]() ![]() ![]() | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
Header (meta data in XML format) |
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Images |
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Archive directory |
-Related structure data
Related structure data | ![]() 4v61CM C: citing same article ( M: atomic model generated by this map |
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Similar-shape strucutres |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.76 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire Spinacea oleracea chloroplast 70S ribosome
Entire | Name: Spinacea oleracea chloroplast 70S ribosome / Number of components: 1 |
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Mass | Theoretical: 2.5 MDa |
-Component #1: ribosome-eukaryote, Spinach Chloroplast 70S Ribosome
Ribosome-eukaryote | Name: Spinach Chloroplast 70S Ribosome / a.k.a: chloro-ribosome Details: The SSU 30S has PSRP1,2,3, and 4 identified. LSU 50S did not have PRPL25 and PRPL30 density present. pRRF (plastid ribosome recycling factor)is tightly bound to LSU 50S subunit. One of the ...Details: The SSU 30S has PSRP1,2,3, and 4 identified. LSU 50S did not have PRPL25 and PRPL30 density present. pRRF (plastid ribosome recycling factor)is tightly bound to LSU 50S subunit. One of the two PSRPs on the LSU 50S subunit is identified. Eukaryote: ALL / Recombinant expression: No |
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Mass | Experimental: 2.5 MDa |
Source | Species: ![]() ![]() |
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Sample solution | Buffer solution: 10mM Tris-HCL pH 7.6, 50mM KCL, 10mM MgOAc, 7mM 2-ME pH: 7.6 |
Support film | quantifoil 300 mesh copper grid |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % Method: 5 microliters applied to the grid then blotted for 3 seconds with Whatman number 1 filter paper before plunging Details: Vitrification instrument: Cryo-plunger |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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![]() | Microscope: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Magnification: 50000 X (nominal), 50760 X (calibrated) Astigmatism: objective lens astigmatism was corrected at 250K times magnification Imaging mode: BRIGHT FIELD ![]() |
Specimen Holder | Holder: Cryo Transfer Holder / Model: OTHER / Temperature: 93 |
Camera | Detector: KODAK SO-163 FILM |
-Image acquisition
Image acquisition | Number of digital images: 164 / Scanner: ZEISS SCAI / Sampling size: 14 µm / Bit depth: 12 |
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Image processing
![]() | Method: ![]() Details: Initially, 192,133 images were selected using automated particle picking program Applied symmetry: C1 (asymmetric) |
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3D reconstruction | Algorithm: Projection matching procedure / Software: SPIDER / CTF correction: each micrograph / Resolution: 9.4 Å / Resolution method: FSC 0.5 |