+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5126 | |||||||||
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Title | In vivo 70S E.coli ribosome with PSRP1 | |||||||||
Map data | 70S E.coli ribosome and PSRP1 in vivo | |||||||||
Sample |
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Keywords | 70S / E.coli Ribosome / Cryo-EM PSRP1 / PSRP-1 / ribosomal protein / stress response factor. | |||||||||
Biological species | Escherichia coli (E. coli) / Spinacia oleracea (spinach) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.1 Å | |||||||||
Authors | Sharma MR / Donhofer A / Barat C / Datta P / Fucini P / Wilson DN / Agrawal RK | |||||||||
Citation | Journal: J Biol Chem / Year: 2010 Title: PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G). Authors: Manjuli R Sharma / Alexandra Dönhöfer / Chandana Barat / Viter Marquez / Partha P Datta / Paola Fucini / Daniel N Wilson / Rajendra K Agrawal / Abstract: Plastid-specific ribosomal proteins (PSRPs) have been proposed to play roles in the light-dependent regulation of chloroplast translation. Here we demonstrate that PSRP1 is not a bona fide ribosomal ...Plastid-specific ribosomal proteins (PSRPs) have been proposed to play roles in the light-dependent regulation of chloroplast translation. Here we demonstrate that PSRP1 is not a bona fide ribosomal protein, but rather a functional homologue of the Escherichia coli cold-shock protein pY. Three-dimensional Cryo-electron microscopic (Cryo-EM) reconstructions reveal that, like pY, PSRP1 binds within the intersubunit space of the 70S ribosome, at a site overlapping the positions of mRNA and A- and P-site tRNAs. PSRP1 induces conformational changes within ribosomal components that comprise several intersubunit bridges, including bridge B2a, thereby stabilizes the ribosome against dissociation. We find that the presence of PSRP1/pY lowers the binding of tRNA to the ribosome. Furthermore, similarly to tRNAs, PSRP1/pY is recycled from the ribosome by the concerted action of the ribosome-recycling factor (RRF) and elongation factor G (EF-G). These results suggest a novel function for EF-G and RRF in the post-stress return of PSRP1/pY-inactivated ribosomes to the actively translating pool. | |||||||||
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_5126.map.gz | 7.7 MB | EMDB map data format | |
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Header (meta data) | emd-5126-v30.xml emd-5126.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_5126_1.png | 216.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5126 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5126 | HTTPS FTP |
-Validation report
Summary document | emd_5126_validation.pdf.gz | 78 KB | Display | EMDB validaton report |
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Full document | emd_5126_full_validation.pdf.gz | 77.1 KB | Display | |
Data in XML | emd_5126_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5126 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5126 | HTTPS FTP |
-Related 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_5126.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 70S E.coli ribosome and PSRP1 in vivo | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : In vivo 70S E.coli ribosome with PSRP1
Entire | Name: In vivo 70S E.coli ribosome with PSRP1 |
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Components |
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-Supramolecule #1000: In vivo 70S E.coli ribosome with PSRP1
Supramolecule | Name: In vivo 70S E.coli ribosome with PSRP1 / type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Experimental: 2.8 MDa / Theoretical: 2.8 MDa |
-Supramolecule #1: 70S Ribosome
Supramolecule | Name: 70S Ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: LSU 50S, SSU 30S |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 2.5 MDa / Theoretical: 2.5 MDa |
-Macromolecule #1: plastid specific ribosomal protein-1
Macromolecule | Name: plastid specific ribosomal protein-1 / type: ligand / ID: 1 / Name.synonym: PSRP1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Spinacia oleracea (spinach) / synonym: Spinach / Organelle: chloroplast |
Molecular weight | Experimental: 270 KDa / Theoretical: 270 KDa |
-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: 20mM Hepes-KOH, 8.2mM MgCl2, 80mM NH4Cl, 4mM beta-mercaptoethanol |
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Grid | Details: 300 mesh coper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Plunger / Method: Blot for 3 seconds then plunge |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 37 / Average electron dose: 24 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: 4.3 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each Micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 18317 |
Final two d classification | Number classes: 15 |