REL PDBe PDBe PDBe 2002-10-08 2002-10-09 2002-10-09 2016-06-29 Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid. San Martin C Huiskonen JT Bamford JK Butcher SJ Fuller SD Bamford DH Burnett RM San Martin C Huiskonen JT Bamford JK Butcher SJ Fuller SD Bamford DH Burnett RM Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid. NAT.STRUCT.BIOL. 9 756 763 2002 12219080 doi:10.1038/nsb837 1gw7 FULLOVERLAP Bacteriophage PRD1 Bacteriophage PRD1
The sample is a virion containing at least 19 structural proteins and a double stranded DNA genome
A pseudo T=25 assembly 1 70 Enterobacteria phage PRD1
a T=25 virion
Enterobacteria phage PRD1 Salmonella enterica BACTERIA(EUBACTERIA) P3 70 25 VIRION STRAIN false false 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 1 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 50 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 16.0 OTHER EMBL-ICOS, MRC
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.
1468
range giving min eigenvalues for inversion of less than .01
 emd_1011.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 -127 -127 -127 256 256 256 880.64 880.64 880.64 90 90 90 X Y Z -16843.700000000000728 27000.0 188.24799999999999 3602.7199999999998 3.44 3.44 3.44 7770.0 This map is one of four described in 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. The other three maps are also available.
::::EMDATABANK.org::::EMD-1011::::
 1GW7 A B C D E F G H I RIGID BODY FIT 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: real space refinement. 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
minimizing R factor (final 47.7%) REAL emd_1011_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 -15940.523440000000846 24043.013670000000275 656.550230000000056 0.0 3.44 3.44 3.44
Created by IMAGIC: MRC image = /ebi/msd/emdeposit/submissions/EMD-1210/UP/tempCC P4/m 09-10-20 13:30:08
 emd_1011_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 -15709.902340000000549 24138.25 652.497560000000021 0.0 3.44 3.44 3.44
Created by IMAGIC: MRC image = /ebi/msd/emdeposit/submissions/EMD-1210/UP/tempCC P4/m 09-10-20 13:31:02
 emd_1011_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 -15620.572270000000572 24412.707030000001396 653.292910000000006 0.0 3.44 3.44 3.44
Created by IMAGIC: MRC image = /ebi/msd/emdeposit/submissions/EMD-1210/UP/tempCC P4/m 09-10-20 13:31:39