Journal: J Mol Biol / Year: 2011 Title: Stepwise expansion of the bacteriophage ϕ6 procapsid: possible packaging intermediates. Authors: Daniel Nemecek / Naiqian Cheng / Jian Qiao / Leonard Mindich / Alasdair C Steven / J Bernard Heymann / Abstract: The initial assembly product of bacteriophage ϕ6, the procapsid, undergoes major structural transformation during the sequential packaging of its three segments of single-stranded RNA. The ...The initial assembly product of bacteriophage ϕ6, the procapsid, undergoes major structural transformation during the sequential packaging of its three segments of single-stranded RNA. The procapsid, a compact icosahedrally symmetric particle with deeply recessed vertices, expands to the spherical mature capsid, increasing the volume available to accommodate the genome by 2.5-fold. It has been proposed that expansion and packaging are linked, with each stage in expansion presenting a binding site for a particular RNA segment. To investigate procapsid transformability, we induced expansion by acidification, heating, and elevated salt concentration. Cryo-electron microscopy reconstructions after all three treatments yielded the same partially expanded particle. Analysis by cryo-electron tomography showed that all vertices of a given capsid were either in a compact or an expanded state, indicating a highly cooperative transition. To benchmark the mature capsid, we analyzed filled (in vivo packaged) capsids. When these particles were induced to release their RNA, they reverted to the same intermediate state as expanded procapsids (intermediate 1) or to a second, further expanded state (intermediate 2). This partial reversibility of expansion suggests that the mature spherical capsid conformation is obtained only when sufficient outward pressure is exerted by packaged RNA. The observation of two intermediates is consistent with the proposed three-step packaging process. The model is further supported by the observation that a mutant capable of packaging the second RNA segment without previously packaging the first segment has enhanced susceptibility for switching spontaneously from the procapsid to the first intermediate state.
History
Deposition
Nov 28, 2011
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Header (metadata) release
May 23, 2012
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Map release
May 23, 2012
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Update
May 23, 2012
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Current status
May 23, 2012
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_5356.map.gz / Format: CCP4 / Size: 65.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
This is expansion intermediate of the bacteriophage phi6 procapsid that was obtained by RNA release from already packaged capsids.
Voxel size
X=Y=Z: 2.62792 Å
Density
Contour Level
By EMDB: 1.62 / Movie #1: 1.5
Minimum - Maximum
-4.86563253 - 6.11769676
Average (Standard dev.)
0.0 (±1.0)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
-130
-130
-130
Dimensions
260
260
260
Spacing
260
260
260
Cell
A=B=C: 683.25916 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.6279192307692
2.6279192307692
2.6279192307692
M x/y/z
260
260
260
origin x/y/z
0.000
0.000
0.000
length x/y/z
683.259
683.259
683.259
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-62
-62
-62
NX/NY/NZ
125
125
125
MAP C/R/S
1
2
3
start NC/NR/NS
-130
-130
-130
NC/NR/NS
260
260
260
D min/max/mean
-4.866
6.118
0.000
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Supplemental data
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Sample components
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Entire : Expansion Intermediate 2 of the P1247 Procapsid of Bacteriophage phi6
Entire
Name: Expansion Intermediate 2 of the P1247 Procapsid of Bacteriophage phi6
Components
Sample: Expansion Intermediate 2 of the P1247 Procapsid of Bacteriophage phi6
Virus: Bacteriophage phi6 (bacteriophage)
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Supramolecule #1000: Expansion Intermediate 2 of the P1247 Procapsid of Bacteriophage phi6
Supramolecule
Name: Expansion Intermediate 2 of the P1247 Procapsid of Bacteriophage phi6 type: sample / ID: 1000 Oligomeric state: Icosahedral shell of P1 dimers with P2, P4 and P7 subunits Number unique components: 4
Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Date
Sep 23, 2008
Image recording
Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 52 / Average electron dose: 15 e/Å2 / Bits/pixel: 16
Electron beam
Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
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