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Title:Three-dimensional structures of translating ribosomes by Cryo-EM.
Authors:R.J.C.Gilbert, P.Fucini, S.Connell, S.D.Fuller, K.H.Nierhaus, C.V.Robinson, C.M.Dobson, D.I.Stuart
Sample:E. coli ribosome translating GFP
Aggregation state:Single particle (16 angstroms resolution)
Red flagLatest update:2011-05-26
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Sample
Sample name: E. coli ribosome translating GFP
Oligomeric state: 30S subunit and 50S subunit, 2 tRNA molecules and 1 nascent protein
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism GO identifier InterPro identifier Virus identifier Details
1ribosome-prokaryoteE. coli 30S subunit
2ribosome-prokaryoteE. coli 50S subunit
3nucleic-acidP site tRNAfalseEscherichia colipartial occupancy
4nucleic-acidE site tRNAfalseEscherichia colipartial occupancy lower than P site
5proteinGreen fluorescent proteinMonomertrueunidentified
Experiment
Sample preparation:
pHSample conc.DetailsStainingSample support details
5.0 mg/mL20 mM HEPES, 150 mM ammonium acetate, 6 mM magnesium acetate, 2 mM spermidine, 0.05 mM spermine and 4 mM 2-mercaptoethanol. Concentration of ribosomes expressed to A260 units.300 mesh copper grid with holey carbon film
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE%100 KHOMEMADE PLUNGER msVitrification instrument: Standard unmodified guillotine plunger
Imaging:
MicroscopeVoltageIllumination modeImaging modeCs:Defocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI/PHILIPS CM200FEG200 kVOTHEROTHER2 mm1805 nm5960 nm50000FIELD EMISSION GUNKodak SO163 film mm

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
EucentricGATAN LIQUID NITROGEN°° eV100 K K K mrad e/Å22000-05-02
Processing
Software:SPIDER, IMAGIC, GAP, CNS, XPLOR
CTF correction:Each negative dataset
Resolution by author:16 Å
Resolution method:FSC at 0.5 cut-off
Processing details:Final maps were calculated from 2276 images from a total of 4500 from 10 individual datasets, with scaling in reciprocal space to crystallographic ribosome structures and correction for map anisotropy by B-factor weighting of amplitudes in XPLOR with respect to a similarly-treated control inactive ribosome. Selection of particles for inclusion in the final maps was by correlation coefficient with respect to the alignment model, designed to maximise nascent chain occupancy in the selected images.
Unit cell:
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
108.322 μm/pixel58linkScanner model:UMAX PowerLook 3000OTHER
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
Rigid bodyR-factor and correlation coefficientGAPREAL
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