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- EMDB-5265: Intermediate states observed in the pre-translocation ribosome du... -

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Basic information

Database: EMDB / ID: 5265
TitleIntermediate states observed in the pre-translocation ribosome during tRNA translocation
Keywordsribosome / translocation / tRNA
Samplepre-translocation ribosome complex
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataE. coli ribosome: rotated structure
Methodsingle particle reconstruction, at 13.2 Å resolution
AuthorsFu J / Munro J / Blanchard SC / Frank J
CitationProc. Natl. Acad. Sci. U.S.A., 2011, 108, 4817-4821

Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 4817-4821 Yorodumi Papers
Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
Jie Fu / James B Munro / Scott C Blanchard / Joachim Frank

DateDeposition: Feb 25, 2011 / Header (metadata) release: Feb 28, 2011 / Map release: Feb 28, 2011 / Last update: Mar 6, 2013

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 50
  • Imaged by UCSF CHIMERA
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3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_5265.map.gz (map file in CCP4 format, 7631 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
125 pix
3 Å/pix.
= 375. Å
125 pix
3 Å/pix.
= 375. Å
125 pix
3 Å/pix.
= 375. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3 Å
Contour Level:50 (by author), 50 (movie #1):
Minimum - Maximum-124.09147644 - 251.13751221
Average (Standard dev.)4.70021105 (26.03857613)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 375 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z333
M x/y/z125125125
origin x/y/z0.0000.0000.000
length x/y/z375.000375.000375.000
start NX/NY/NZ-62-62-62
MAP C/R/S123
start NC/NR/NS-62-62-62
D min/max/mean-124.091251.1384.700

Supplemental data

Sample components

Entire pre-translocation ribosome complex

EntireName: pre-translocation ribosome complex / Number of components: 3
MassTheoretical: 2.5 MDa

Component #1: ribosome-prokaryote, ribosome

Ribosome-prokaryoteName: ribosome / Prokaryote: ALL / Recombinant expression: No
MassTheoretical: 2.5 MDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

Experimental details

Sample preparation

Specimen stateparticle
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: blot for 8 seconds / Details: Vitrification instrument: vitrobot

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 24 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 100000 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 2500 - 4500 nm
Specimen HolderHolder: cartridge / Model: OTHER / Temperature: 82 K
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 4 / Applied symmetry: C1 (asymmetric) / Number of projections: 84000
3D reconstructionAlgorithm: reference-based projection matching / Software: SPIDER / CTF correction: defocus group and wiener filter / Resolution: 13.2 Å / Resolution method: FSC 0.5

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