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Title:The PM2 virion has a novel organization with an internal membrane and pentameric receptor binding spikes.
Authors:J.T. Huiskonen, H.M. Kivela, D.H. Bamford, S.J. Butcher
Sample:Bromelain-treated PM2 virus
Aggregation state:Icosahedral (13.4 angstroms resolution)
Red flagLatest update:2011-05-26
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Sample
Sample name: Bromelain-treated PM2 virus
Theoretical molecular weight of the sample: 31.9
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism GO identifier InterPro identifier Virus identifier Details
1virusbromelain-treated PM245.1bromelain-treated PM220.0.1.0.001includes mass of DNA,. lipid and proteins
Experiment
Sample preparation:
pHSample conc.DetailsStainingSample support details
7.24 mg/mLCaCl2, 5mM Tris-HCl, 10-20 mM NaCl, 25-125 mM400 mesh copper grid, R2/2 quantifoil holey
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE%90 KHOMEMADE PLUNGERA small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot off excess buffer, sufficient to leave a thin layer on the grid. The filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed in liquid nitrogen for later use in the microscope. msVitrification instrument: EMBL design
Imaging:
MicroscopeVoltageIllumination modeImaging modeCs:Defocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI TECNAI F20200 kVFLOOD BEAMBRIGHT FIELD2 mm1100 nm2000 nm50000FIELD EMISSION GUNkodak SO163 film mmobjective lens astigmatism was corrected at

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
Side entry liquid nitrogen-cooled cryo specimen holderGATAN LIQUID NITROGEN°° eV93 K90 K94 K mrad10 e/Å2A box anticontaminator was fitted with a minimum achievable temperature of 88 K
Processing
Software:EMBL, P3DR
CTF correction:each particle, wiener factor 0.1
Resolution by author:13.4 Å
Resolution method:FSC at 0.5 cut-off
Processing details:reconstruction was in cartesian coordinates applying icosahedral symmetry
Unit cell:
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
157 μm/pixel12linkZEISS SCAI
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
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