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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
1gw8
FULLOVERLAP
Bacteriophage PRD1 sus607 mutant
Bacteriophage PRD1 sus607 mutant
The sample is a virion containing at least 19 structural
proteins and a double stranded DNA genome. This map is from the
sus607 mutant and lacks protein P11
A pseudo T=25 assembly
1
70
Enterobacteria phage PRD1
a T=25 virion
Enterobacteria phage PRD1
Salmonella enterica
BACTERIA(EUBACTERIA)
capsid (contains proteins P3 and P30)
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
0.77
4.13
50000.0
GATAN LIQUID NITROGEN
105
2001-11-01
KODAK SO-163 FILM
ZEISS SCAI
7.0
15
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
13.4
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.
1729
range giving min eigenvalues for inversion of
less than .01
1GW8
A
B
C
D
E
F
G
H
I
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: ridgid body. The scale of the map and the effective resolution were determined from a comparison between the P3 portion of the sus607 reconstruction and the atomic model
minimizing R factor (final 47.7%)
RECIPROCAL
100.0
emd_1012_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
-20772.021479999999428
26672.761719999998604
667.502010000000041
0.0
3.42
3.42
3.42
Created by IMAGIC: MRC image =
/ebi/msd/emdeposit/submissions/EMD-1233/UP/tempCC P4/m
10-10-20 13:57:52
emd_1012_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
-20771.794920000000275
26672.646479999999428
667.50640999999996
0.0
3.42
3.42
3.42
Created by IMAGIC: MRC image =
/ebi/msd/emdeposit/submissions/EMD-1233/UP/tempCC P4/m
10-10-20 13:58:24
emd_1012_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
-20771.679690000000846
26672.605469999998604
667.504209999999944
0.0
3.42
3.42
3.42
Created by IMAGIC: MRC image =
/ebi/msd/emdeposit/submissions/EMD-1233/UP/tempCC P4/m
10-10-20 13:58:52