REL PDBe PDBe PDBe 2002-10-09 2002-06-05 2002-10-10 2015-08-12 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 STRUCTURE 9 917 930 2001 11591347 doi:10.1016/S0969-2126(01)00642-6 1hb7 FULLOVERLAP 1hb9 FULLOVERLAP Bacteriophage PRD1 sus1 mutant Bacteriophage PRD1 sus1 mutant

The sample is a mutant virion containing at least 18 structural proteins. This mutant does not package the dsDNA genome.

A pseudo T=25 assembly 1 70 Enterobacteria phage PRD1

a T=25 virion

Enterobacteria phage PRD1 Salmonella enterica BACTERIA(EUBACTERIA) capsid (P8 and P30 shell) 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

the images are taken a underfocused although the entry indicates a positive defocus value

KODAK SO-163 FILM ZEISS SCAI 7.0 29 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

normalized sum of ctf multiplied images

I OTHER 14.0 OTHER EMBL-ICOS, MRC

final maps were calculated as a normalized sum of image ffts using the svd versions of matbg and then normalized using an overall profile de Haas, F., Paatero, A. O., Mindich,L., Bamford, D. H. and Fuller, S. D. (1999). A symmetry mismatch at the site of RNA packaging by the polymerase complex of dsRNA bacteriophage phi-6. Journal of Molecular Biology 294, 357-372. 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. 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, 917-30. 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.

1800

range giving min eigenvalues for inversion of less than 0.01

1HB7 A B C D E F G H I J K L RIGID BODY FIT X-plor and 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 and clashes RECIPROCAL 150.0 emd_1013_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 -3.82561 7.91972 0.08893 0.0 3.44 3.44 3.44

Created by IMAGIC: MRC image = /ebi/msd/emdeposit/submissions/EMD-1234/UP/tempCC P4/m 10-10-20 14:00:52

emd_1013_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 -3.7101 7.71027 0.08682 0.0 3.44 3.44 3.44

Created by IMAGIC: MRC image = /ebi/msd/emdeposit/submissions/EMD-1234/UP/tempCC P4/m 10-10-20 14:01:16

emd_1013_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 -3.68088 7.85831 0.08902 0.0 3.44 3.44 3.44

Created by IMAGIC: MRC image = /ebi/msd/emdeposit/submissions/EMD-1234/UP/tempCC P4/m 10-10-20 14:01:45