top_cornerHomeEMD-1071  Contact us 
Image unavailable
Title:Three-dimensional structures of translating ribosomes by Cryo-EM.
Authors:Gilbert RJ, Fucini P, Connell S, Fuller SD, Nierhaus KH, Robinson CV, Dobson CM, Stuart DI
Sample:E. coli ribosome translating 2 Ig domains
Aggregation state:Single particle (13.2 angstroms resolution)
Red flagLatest update:2011-05-26
inner_corner
Sample
Sample name: E. coli ribosome translating 2 Ig domains
Oligomeric state: 30S subunit and 50S subunit, 2 tRNA molecules, 1 nascent protein and 1 Ig nascent polypeptide
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Mutant Organism GO identifier InterPro identifier Virus identifier Details
1ribosome-prokaryoteE. coli 30S subunit
2ribosome-prokaryoteE. coli 50S subunit
3nucleic-acidP site tRNAfalseE. colipartial occupancy
4nucleic-acidE site tRNAfalseE. colipartial occupancy lower than P site
5proteinTandem Ig domains of D. discoideum ABPMonomertrueDistyostelium discoideum
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 KStandard unmodified guillotine plunger ms
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI/PHILIPS CM200FEG200 kVOTHEROTHER2 mm1620 nm3490 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/Å22000-05-01
Processing
Software:SPIDER, IMAGIC, GAP, CNS, XPLOR
CTF correction:Each negative dataset
Resolution by author:13.2 Å
Resolution method:FSC at 0.5 cut-off
Processing details:Final maps were calculated from 4434 images from a total of 8898 from 14 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
148.322 μm/pixel58linkOTHER
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
Rigid bodyR-factor and correlation coefficientGAPREAL
outer_corner