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Title:Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid.
Authors:San Martin C, Huiskonen JT, Bamford JK, Butcher SJ, Fuller SD, Bamford DH, Burnett RM
Sample:Bacteriophage PRD1
Aggregation state:Icosahedral (16 angstroms resolution)
Red flagLatest update:2011-05-26
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Sample
Sample name: Bacteriophage PRD1
Oligomeric state: A pseudo T=25 assembly
Theoretical molecular weight of the sample: 70
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Mutant Organism GO identifier InterPro identifier Virus identifier Details
1virusPRD1PRD1a T=25 virion
Experiment
Sample preparation:
pHSample conc.DetailsStainingSample support details
7.21 mg/mL20 mM Tris HCl
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE60%23 KEMBL plungerBlot for 1 s before plunging into ethane slush msvitrification carried out at 23 degrees at ambient humidity
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI/PHILIPS CM200FEG/ST200 kVFLOOD BEAMBRIGHT FIELD2 mm1300 nm4100 nm36000FIELD EMISSION GUNSO16344 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 mrad6 e/Å2
Processing
Software:EMBL-ICOS, MRC
CTF correction:normalized sum of ctf multiplied images
Resolution by author:16 Å
Resolution method:16
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. Butcher, S. J., Bamford, D. H., and Fuller, S. D. (1995). DNA packaging orders the membrane of bacteriophage PRD1. Embo J 14, 6078-6086. Ferlenghi, I., Gowen, B., de Haas, F., Mancini, E. J., Garoff, H., Sjoberg, M., and Fuller, S. D. (1998). The first step: activation of the Semliki Forest virus spike protein precursor causes a localized conformational change in the trimeric spike. J Mol Biol 283, 71-81. Fuller, S. D., Berriman, J. A., Butcher, S. J., and Gowen, B. E. (1995). Low pH induces swiveling of the glycoprotein heterodimers in the Semliki Forest virus spike complex. Cell 81, 715-725. 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. San Martin, C., Burnett, R. M., de Haas, F., Heinkel, R., Rutten, T., Fuller, S. D., Butcher, S. J., and Bamford, D. H. (2001). Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. Structure (Camb) 9, 917-930. San Martin, C., Huiskonen, J. T., Bamford, J. K., Butcher, S. J., Fuller, S. D., Bamford, D. H., and Burnett, R. M. (2002). Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid. Nat Struct Biol 9, 756-763. Sheehan, B., Fuller, S. D., Pique, M. E., and Yeager, M. (1996). AVS software for visualization in molecular microscopy. J Struct Biol 116, 99-106.
Unit cell:
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
507.0 μm/pixel18linkimages were scanned at 7 micron steps size and then averaged to give a final size of 14 micronsZEISS SCAI
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
1GW7 real space refinementminimizing R factor (final 47.7%)emfit (M. Rossmann Cheng, R., Kuhn, R., Olson, N., Rossmann, M., and Baker, T. (1995). Nucleocapsid and glycoprotein organization in an enveloped virus. Cell 80, 621-630.)The scale of the map and the effective resolution were determined from a comparison between the P3 portion of the WT reconstruction and the atomic model
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