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PDBsum entry 1cd3
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143 a.a.
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135 a.a.
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426 a.a.
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175 a.a.
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68 a.a.
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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The role of scaffolding proteins in the assembly of the small, Single-Stranded DNA virus phix174.
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Authors
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T.Dokland,
R.A.Bernal,
A.Burch,
S.Pletnev,
B.A.Fane,
M.G.Rossmann.
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Ref.
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J Mol Biol, 1999,
288,
595-608.
[DOI no: ]
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PubMed id
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Abstract
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An empty precursor particle called the procapsid is formed during assembly of
the single-stranded DNA bacteriophage phiX174. Assembly of the phiX174 procapsid
requires the presence of the two scaffolding proteins, D and B, which are
structural components of the procapsid, but are not found in the mature virion.
The X-ray crystallographic structure of a "closed" procapsid particle
has been determined to 3.5 A resolution. This structure has an external scaffold
made from 240 copies of protein D, 60 copies of the internally located B
protein, and contains 60 copies of each of the viral structural proteins F and
G, which comprise the shell and the 5-fold spikes, respectively. The F capsid
protein has a similar conformation to that seen in the mature virion, and
differs from the previously determined 25 A resolution electron microscopic
reconstruction of the "open" procapsid, in which the F protein has a
different conformation. The D scaffolding protein has a predominantly
alpha-helical fold and displays remarkable conformational variability. We report
here an improved and refined structure of the closed procapsid and describe in
some detail the differences between the four independent D scaffolding proteins
per icosahedral asymmetric unit, as well as their interaction with the F capsid
protein. We re-analyze and correct the comparison of the closed procapsid with
the previously determined cryo-electron microscopic image reconstruction of the
open procapsid and discuss the major structural rearrangements that must occur
during assembly. A model is proposed in which the D proteins direct the assembly
process by sequential binding and conformational switching.
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Figure 1.
Figure 1. Stereo representation of
the helical domain of the C
a
back-
bone of the F protein in the procap-
sid structure (red) and the F
protein in the virion (black). The
superimposed b-barrel domain is
colored green in the procapsid
structure and blue in the virion.
Symmetry axes are those in the
virion.
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Figure 9.
Figure 9. View down the 3-fold axis showing the relationship of the F protein as seen in the closed procapsid
when superimposed onto the EM density of the open procapsid. The big hole on the 3-fold axis in the EM reconstruc-
tion of the open procapsid is covered by helix 4 of the F protein in the closed procapsid X-ray structure. Gray and
blue contours represent two density levels in the 25 Å resolution EM structure.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
288,
595-608)
copyright 1999.
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Secondary reference #1
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Title
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Structure of a viral procapsid with molecular scaffolding.
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Authors
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T.Dokland,
R.Mckenna,
L.L.Ilag,
B.R.Bowman,
N.L.Incardona,
B.A.Fane,
M.G.Rossmann.
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Ref.
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Nature, 1997,
389,
308-313.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 C  backbone
plot of the F protein in the closed procapsid (red). The
asymmetric unit triangle is shown, with the symmetry axes
marked. The F-protein structure from the virion (yellow) was
superimposed on the closed procapsid F protein by minimizing the
r.m.s. distance between corresponding C atoms
in the -helical
domain (residues 175-207, 305-319). The main difference in the F
protein between the virion and the closed procapsid is a hinge
movement between the -helical
domain and the  -sandwich
domain. Residues involved in second-site suppression of
cold-sensitive D mutants21 are circled.
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Figure 4.
Figure 4 Structural comparison of the D subunits. Only the C
backbones
are shown. Superposition of the D1 : D2 (green : yellow) dimer
onto the D3 : D4 (red : blue) dimer. (The colour scheme is as in
Fig. 3 .) The superposition was achieved by minimizing the
r.m.s. distance between corresponding C atoms
within the structurally conserved core region. Secondary
structure elements are indicated. The asterisk represents the
kink in 3
of subunits D1 and D3.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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Secondary reference #2
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Title
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Dna packaging intermediates of bacteriophage phi X174.
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Authors
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L.L.Ilag,
N.H.Olson,
T.Dokland,
C.L.Music,
R.H.Cheng,
Z.Bowen,
R.Mckenna,
M.G.Rossmann,
T.S.Baker,
N.L.Incardona.
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Ref.
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Structure, 1995,
3,
353-363.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Assembly pathway of φX174 based on Hayashi et al.
[4]. Figure 1. Assembly pathway of φX174 based on Hayashi et
al. [[3]4].
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Figure 7.
Figure 7. Fit of the F protein pentamer into cryo-EM density of
the procapsid (a) and (b) and provirion (c) and (d), color
coded as described for Figure 5b. The views are down a five-fold
axis (a,c) and from the side (b,d). Only the truncated F
protein is shown, that is the β-barrel without the EF and HI
insertions. Figure 7. Fit of the F protein pentamer into
cryo-EM density of the procapsid (a) and (b) and provirion (c)
and (d), color coded as described for [3]Figure 5b. The views
are down a five-fold axis (a,c) and from the side (b,d). Only
the truncated F protein is shown, that is the β-barrel without
the EF and HI insertions.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #3
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Title
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Analysis of the single-Stranded DNA bacteriophage phi X174, Refined at a resolution of 3.0 a.
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Authors
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R.Mckenna,
L.L.Ilag,
M.G.Rossmann.
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Ref.
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J Mol Biol, 1994,
237,
517-543.
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PubMed id
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Secondary reference #4
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Title
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Atomic structure of single-Stranded DNA bacteriophage phi X174 and its functional implications.
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Authors
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R.Mckenna,
D.Xia,
P.Willingmann,
L.L.Ilag,
S.Krishnaswamy,
M.G.Rossmann,
N.H.Olson,
T.S.Baker,
N.L.Incardona.
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Ref.
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Nature, 1992,
355,
137-143.
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PubMed id
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Secondary reference #5
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Title
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The bacteriophages
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Authors
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M.Hayashi,
A.Aoyama,
L.Delwood,
D.L.Richardson,
M.N.Hayashi.
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Ref.
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the bacteriophages (in: the, 1988,
2,
1.
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Secondary reference #6
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Title
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Nucleotide sequence of bacteriophage phi X174 DNA.
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Authors
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F.Sanger,
G.M.Air,
B.G.Barrell,
N.L.Brown,
A.R.Coulson,
C.A.Fiddes,
C.A.Hutchison,
P.M.Slocombe,
M.Smith.
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Ref.
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Nature, 1977,
265,
687-695.
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PubMed id
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