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Title:Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus.
Authors:E. J. Mancini, M. Clarke, B. Gowen, T. Rutten, S. D. Fuller,
Sample:Semliki Forest Virus
Aggregation state:Icosahedral (9.0 angstroms resolution)
Red flagLatest update:2011-05-26
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Sample
Sample name: Semliki Forest Virus
Oligomeric state: T=4 membraneous particle
Theoretical molecular weight of the sample: 50
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism GO identifier InterPro identifier Virus identifier Details
1virusSemliki forest virusSemliki forest virus73.0.1.0.023
Experiment
Sample preparation:
pHSample conc.DetailsStainingSample support details
7.43 mg/mLTris (10mM) NaCl (100 mM) ph 7.4
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE100%37 KHOMEMADE PLUNGERBlot for 2 sec Graticule grids were used to maintain flatness msVitrification instrument: EMBL plunger with warm humid air spray. plunging at ambient temperature and humidity
Imaging:
MicroscopeVoltageIllumination modeImaging modeCs:Defocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI/PHILIPS CM200FEG/ST200 kVFLOOD BEAMBRIGHT FIELD2 mm975 nm7628 nm50000FIELD EMISSION GUNSO 163 film44 mm

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
eucentricGATAN LIQUID NITROGEN°° eV105 K K K mrad8 e/Å21995-01-01
Processing
Software:EMBL-ICOS
CTF correction:ctf multiplication and summation of normalized reconstructions
Resolution by author:9.0 Å
Resolution method:fsc = 0.5 between independent reconstructions
Processing details:final maps were calculated by making a normalized sum of seperate ctf multiplied maps: Baker, T. S., Olson, N. H., and Fuller, S. D. (1999). Adding the third dimension to virus life cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs. Microbiology and Molecular Biology Reviews 63, 862-922. Fuller, S. D., Butcher, S. J., Cheng, R. H., and Baker, T. S. (1996). Three-dimensional reconstruction of icosahedral particles-the uncommon line. J Struct Biol 116, 48-55. Mancini, E. J., Clarke, M., Gowen, B., Rutten, T., and Fuller, S. D. (2000). Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus. Molecular Cell 5, 255-266. Mancini, E. J., de Haas, F., and Fuller, S. D. (1997). High-resolution icosahedral reconstruction: fulfilling the promise of cryo-electron microscopy. Structure 5, 741-750.
Unit cell:
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
487 μm/pixel18linkZEISS SCAI
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
1DYL rigid bodyR factor and clashesemfit (Cheng et al 1995)REALThe capsid protein used for the rigid body refinement was PDB entry 1VCQ
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