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

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Basic information

Database: EMDB / ID: 5126
TitleIn vivo 70S E.coli ribosome with PSRP1
Keywords70S / E.coli Ribosome / Cryo-EM PSRP1 / PSRP-1 / ribosomal protein / stress response factor.
SampleIn vivo 70S E.coli ribosome with PSRP1
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Spinacia oleracea / plant / spinach / Spinach / ホウレンソウ
Map data70S E.coli ribosome and PSRP1 in vivo
Methodsingle particle reconstruction, at 14.1 Å resolution
AuthorsSharma MR / Donhofer A / Barat C / Datta P / Fucini P / Wilson DN / Agrawal RK
CitationJ. Biol. Chem., 2010, 285, 4006-4014

J. Biol. Chem., 2010, 285, 4006-4014 Yorodumi Papers
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).
Manjuli R Sharma / Alexandra Dönhöfer / Chandana Barat / Viter Marquez / Partha P Datta / Paola Fucini / Daniel N Wilson / Rajendra K Agrawal

DateDeposition: Jul 21, 2009 / Header (metadata) release: May 5, 2010 / Map release: May 5, 2010 / Last update: May 22, 2013

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 30
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 30
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_5126.map.gz (map file in CCP4 format, 8584 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
2.76 Å/pix.
= 358.8 Å
130 pix
2.76 Å/pix.
= 358.8 Å
130 pix
2.76 Å/pix.
= 358.8 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.76 Å
Contour Level:30 (by author), 30 (movie #1):
Minimum - Maximum-118.6785202 - 298.90179443
Average (Standard dev.)3.67785358 (29.2354641)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 358.8 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ-34-26-72
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-118.679298.9023.678

Supplemental data

Sample components

Entire In vivo 70S E.coli ribosome with PSRP1

EntireName: In vivo 70S E.coli ribosome with PSRP1 / Number of components: 2
MassTheoretical: 2.8 MDa / Experimental: 2.8 MDa

Component #1: ribosome-prokaryote, 70S Ribosome

Ribosome-prokaryoteName: 70S Ribosome / Prokaryote: LSU 50S, SSU 30S / Recombinant expression: No
MassTheoretical: 2.5 MDa / Experimental: 2.5 MDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

Component #2: ligand, plastid specific ribosomal protein-1

LigandName: plastid specific ribosomal protein-1 / a.k.a: PSRP1 / Recombinant expression: No
MassTheoretical: 270 kDa / Experimental: 270 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / Spinach / ホウレンソウ
Source (natural)Organelle: chloroplast

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 20mM Hepes-KOH, 8.2mM MgCl2, 80mM NH4Cl, 4mM beta-mercaptoethanol
pH: 7.6
Support film300 mesh coper grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 80 % / Method: Blot for 3 seconds then plunge / Details: Vitrification instrument: Plunger

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 24 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50760 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 1600 - 4300 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 37 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 12

Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 15 / Applied symmetry: C1 (asymmetric) / Number of projections: 18317
3D reconstructionAlgorithm: projection matching / Software: Spider / CTF correction: Each Micrograph / Resolution: 14.1 Å / Resolution method: FSC 0.5

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