REL PDBe PDBe PDBe 2002-10-09 2002-06-05 2002-10-10 2015-08-12 Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. San Martin C Burnett RM de Haas F Heinkel R Rutten T Fuller SD Butcher SJ Bamford DH Martin CS Burnett RM de Haas F Heinkel R Rutten T Fuller SD Butcher SJ Bamford DH Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. STRUCTURE 9 917 930 2001 11591347 doi:10.1016/S0969-2126(01)00642-6 1hb5 FULLOVERLAP 1hb9 FULLOVERLAP Bacteriophage PRD1 P3 shell Bacteriophage PRD1 P3 shell
The sample is 180 trimers of the P3 protein(43.1kD). produced by treatment of the sus1 mutant with SDS to remove the non-P3 proteins and the pentonal P3 trimers.Recent evidence indicates that some protein P30 is associated with the shell
A pseudo T=25 assembly 1 23.274 theoretical 180*3*43.1 kD Enterobacteria phage PRD1
a T=25 virion. PRD1 P3 shell
Enterobacteria phage PRD1 Salmonella enterica BACTERIA(EUBACTERIA) P3 (contains some P30) 70 25 VIRION STRAIN false true bacteriophage PRD1 singleParticle particle 1 7.2
20 mM Tris HCl
 ETHANE 60 23 HOMEMADE PLUNGER
Vitrification instrument: EMBL plunger. vitrification carried out at 23 degrees at ambient humidity
Blot for 2 s before plunging into ethane slush FEI/PHILIPS CM200FEG/ST FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2 1.3 4.1 36000.0 GATAN LIQUID NITROGEN 105 KODAK SO-163 FILM ZEISS SCAI 7.0 5 6 44
images were scanned at 7 micron steps size and then averaged to give a final size of 14 microns
1.0 8. eucentric
The particles were purified by rate-zonal centrifugation and ion-exchange chromatography Walin,Tuma,Thomas and Bamford Virology (1994) 201:1-7 and then SDS treated to leave the shell.
normalized sum of ctf multiplied images
 I OTHER 12.0 OTHER EMBL-ICOS, MRC
final maps were calculated by making a normalized sum of seperate ctf multiplied maps as 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.
471
range giving inverse eigenvalues for inversion of less than .01 in BG
 emd_1014.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 -127 -127 -127 256 256 256 867.84 867.84 867.84 90 90 90 X Y Z -4.33931 9.01169 0.00187538 0.999844 3.39 3.39 3.39 1.8 This is the structure of the P3 shell of PRD1 produced by treatment of the sus1 mutant with SDS.
::::EMDATABANK.org::::EMD-1014::::
 1HB5 A B C D E F G H I RIGID BODY FIT X-plor, 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.)
Protocol: rigid body refinement. The amplitude and distance scales were determined by comparison with an initial quasi atomic model
minimizing R factor (final 47.7%) REAL 150.0 emd_1014_1_slc.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 1 -127 -127 0 256 256 0 256.000 256.000 1.000 90.000 90.000 90.000 X Y Z -3.90472 8.164759999999999 0.05336 0.0 3.39 3.39 3.39
LABEL Mode 2: Linear Stretch A,B = 1.0000 0.0000 // Created by IMAGIC : MRC image = /ebi/msd/emdeposit/submissions/EMD-1235/UP/tempCCP4/m 10-10-20 14 :32:08 //
 emd_1014_2_slc.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 1 -127 -127 0 256 256 0 256.000 256.000 1.000 90.000 90.000 90.000 X Y Z -3.91973 8.33123 0.04878 0.0 3.39 3.39 3.39
Created by IMAGIC: MRC image = /ebi/msd/emdeposit/submissions/EMD-1235/UP/tempCC P4/m 10-10-20 14:33:07
 emd_1014_3_slc.map 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 1 -127 -127 0 256 256 0 256.000 256.000 1.000 90.000 90.000 90.000 X Y Z -3.87259 8.17259 0.04781 0.0 3.39 3.39 3.39
Created by IMAGIC: MRC image = /ebi/msd/emdeposit/submissions/EMD-1235/UP/tempCC P4/m 10-10-20 14:33:57