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- EMDB-5126: In vivo 70S E.coli ribosome with PSRP1 -

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Basic information

Entry
Database: EMDB / ID: EMD-5126
TitleIn vivo 70S E.coli ribosome with PSRP1
Map data70S E.coli ribosome and PSRP1 in vivo
Sample
  • Sample: In vivo 70S E.coli ribosome with PSRP1
  • Complex: 70S RibosomeRibosome
  • Ligand: plastid specific ribosomal protein-1
Keywords70S / E.coli Ribosome / Cryo-EM PSRP1 / PSRP-1 / ribosomal protein / stress response factor.
Biological speciesEscherichia coli (E. coli) / Spinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.1 Å
AuthorsSharma MR / Donhofer A / Barat C / Datta P / Fucini P / Wilson DN / Agrawal RK
CitationJournal: 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
DepositionJul 21, 2009-
Header (metadata) releaseMay 5, 2010-
Map releaseMay 5, 2010-
UpdateMay 22, 2013-
Current statusMay 22, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 30
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 30
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5126.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation70S E.coli ribosome and PSRP1 in vivo
Voxel sizeX=Y=Z: 2.76 Å
Density
Contour LevelBy AUTHOR: 30.0 / Movie #1: 30
Minimum - Maximum-118.678520199999994 - 298.901794429999995
Average (Standard dev.)3.67785358 (±29.235464100000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions130130130
Spacing130130130
CellA=B=C: 358.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z358.800358.800358.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
D min/max/mean-118.679298.9023.678

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Supplemental data

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Sample components

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Entire : In vivo 70S E.coli ribosome with PSRP1

EntireName: In vivo 70S E.coli ribosome with PSRP1
Components
  • Sample: In vivo 70S E.coli ribosome with PSRP1
  • Complex: 70S RibosomeRibosome
  • Ligand: plastid specific ribosomal protein-1

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Supramolecule #1000: In vivo 70S E.coli ribosome with PSRP1

SupramoleculeName: In vivo 70S E.coli ribosome with PSRP1 / type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 2.8 MDa / Theoretical: 2.8 MDa

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Supramolecule #1: 70S Ribosome

SupramoleculeName: 70S Ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: LSU 50S, SSU 30S
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightExperimental: 2.5 MDa / Theoretical: 2.5 MDa

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Macromolecule #1: plastid specific ribosomal protein-1

MacromoleculeName: plastid specific ribosomal protein-1 / type: ligand / ID: 1 / Name.synonym: PSRP1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Spinacia oleracea (spinach) / synonym: Spinach / Organelle: chloroplast
Molecular weightExperimental: 270 KDa / Theoretical: 270 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
Details: 20mM Hepes-KOH, 8.2mM MgCl2, 80mM NH4Cl, 4mM beta-mercaptoethanol
GridDetails: 300 mesh coper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Plunger / Method: Blot for 3 seconds then plunge

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50760 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.3 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: 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
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each Micrograph
Final two d classificationNumber classes: 15
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 18317

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