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Yorodumi- EMDB-1417: Cryo-EM study of the Spinach chloroplast ribosome reveals the str... -
+Open data
-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 | |||||||||
Map data | Spinach Chloroplast 70S ribosome | |||||||||
Sample |
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Function / homology | Function and homology information plastid small ribosomal subunit / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / maturation of LSU-rRNA / chloroplast / DNA-templated transcription termination / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...plastid small ribosomal subunit / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / mitochondrial translation / maturation of LSU-rRNA / chloroplast / DNA-templated transcription termination / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / 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: 9.4 Å | |||||||||
Authors | Sharma MR / Wilson DN / Datta PP / Barat C / Schluenzen F / Fucini P / Agrawal RK | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2007 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1417.map.gz | 7.6 MB | EMDB map data format | |
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Header (meta data) | emd-1417-v30.xml emd-1417.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | 1417-3BBN-3BBO.png EMD-1417.tif | 266 KB 744.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1417 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1417 | HTTPS FTP |
-Validation report
Summary document | emd_1417_validation.pdf.gz | 342.8 KB | Display | EMDB validaton report |
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Full document | emd_1417_full_validation.pdf.gz | 342.3 KB | Display | |
Data in XML | emd_1417_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1417 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1417 | HTTPS FTP |
-Related structure data
Related structure data | 4v61MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1417.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Spinach Chloroplast 70S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Spinacea oleracea chloroplast 70S ribosome
Entire | Name: Spinacea oleracea chloroplast 70S ribosome |
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Components |
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-Supramolecule #1000: Spinacea oleracea chloroplast 70S ribosome
Supramolecule | Name: Spinacea oleracea chloroplast 70S ribosome / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 2.5 MDa |
-Supramolecule #1: Spinach Chloroplast 70S Ribosome
Supramolecule | Name: Spinach Chloroplast 70S Ribosome / type: complex / ID: 1 / Name.synonym: 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. Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Spinacia oleracea (spinach) / synonym: Spinach |
Molecular weight | Experimental: 2.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Details: 10mM Tris-HCL pH 7.6, 50mM KCL, 10mM MgOAc, 7mM 2-ME |
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Grid | Details: quantifoil 300 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Cryo-plunger Method: 5 microliters applied to the grid then blotted for 3 seconds with Whatman number 1 filter paper before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 93 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 250K times magnification |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 164 / Average electron dose: 20 e/Å2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50760 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.4 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Cryo Transfer Holder / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Initially, 192,133 images were selected using automated particle picking program |
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CTF correction | Details: each micrograph |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 86370 |
Final two d classification | Number classes: 83 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: O |
Details | Protocol: Rigid Body. Docking of crystallographic structures in 3D map was performed using program O |
Refinement | Protocol: RIGID BODY FIT |
Output model | PDB-4v61: |