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

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Basic information

Entry
Database: EMDB / ID: EMD-5265
TitleIntermediate states observed in the pre-translocation ribosome during tRNA translocation
Map dataE. coli ribosome: rotated structure
Sample
  • Sample: pre-translocation ribosome complex
  • Complex: ribosome
Keywordsribosome / translocation / tRNA
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.2 Å
AuthorsFu J / Munro J / Blanchard SC / Frank J
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
Authors: Jie Fu / James B Munro / Scott C Blanchard / Joachim Frank /
Abstract: mRNA-tRNA translocation is a central and highly regulated process during translational elongation. Along with the mRNA, tRNA moves through the ribosome in a stepwise fashion. Using cryoelectron ...mRNA-tRNA translocation is a central and highly regulated process during translational elongation. Along with the mRNA, tRNA moves through the ribosome in a stepwise fashion. Using cryoelectron microscopy on ribosomes with a P-loop mutation, we have identified novel structural intermediates likely to exist transiently during translocation. Our observations suggest a mechanism by which the rate of translocation can be regulated.
History
DepositionFeb 25, 2011-
Header (metadata) releaseFeb 28, 2011-
Map releaseFeb 28, 2011-
UpdateMar 6, 2013-
Current statusMar 6, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • 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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5265_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5265.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli ribosome: rotated structure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3 Å/pix.
x 125 pix.
= 375. Å		3 Å/pix.
x 125 pix.
= 375. Å		3 Å/pix.
x 125 pix.
= 375. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 50.0 / Movie #1: 50
Minimum - Maximum-124.091476439999994 - 251.137512210000011
Average (Standard dev.)4.70021105 (±26.038576129999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-62-62-62
Dimensions125125125
Spacing125125125
CellA=B=C: 375.0 Å
α=β=γ: 90.0 °

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
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-62-62-62
NC/NR/NS125125125
D min/max/mean-124.091251.1384.700

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Supplemental data

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Sample components

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Entire : pre-translocation ribosome complex

EntireName: pre-translocation ribosome complex
Components
  • Sample: pre-translocation ribosome complex
  • Complex: ribosome

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Supramolecule #1000: pre-translocation ribosome complex

SupramoleculeName: pre-translocation ribosome complex / type: sample / ID: 1000 / Number unique components: 3
Molecular weightTheoretical: 2.5 MDa

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Supramolecule #1: ribosome

SupramoleculeName: ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 2.5 MDa

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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

VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: vitrobot / Method: blot for 8 seconds

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureAverage: 82 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder: cartridge / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: defocus group and wiener filter
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 84000
Final two d classificationNumber classes: 4

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