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References listed in PDB file
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Key reference
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Title
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Functional and evolutionary insight from the crystal structure of rubella virus protein e1.
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Authors
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R.M.Dubois,
M.C.Vaney,
M.A.Tortorici,
R.A.Kurdi,
G.Barba-Spaeth,
T.Krey,
F.A.Rey.
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Ref.
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Nature, 2013,
493,
552-556.
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PubMed id
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Abstract
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No abstract given.
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Secondary reference #1
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Title
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The fusion glycoprotein shell of semliki forest virus: an icosahedral assembly primed for fusogenic activation at endosomal ph.
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Authors
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J.Lescar,
A.Roussel,
M.W.Wien,
J.Navaza,
S.D.Fuller,
G.Wengler,
G.Wengler,
F.A.Rey.
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Ref.
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Cell, 2001,
105,
137-148.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Conformational change and protein-Protein interactions of the fusion protein of semliki forest virus.
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Authors
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D.L.Gibbons,
M.C.Vaney,
A.Roussel,
A.Vigouroux,
B.Reilly,
J.Lepault,
M.Kielian,
F.A.Rey.
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Ref.
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Nature, 2004,
427,
320-325.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3: A ring of five trimers of E1*. a, b, Surface
representation of the ring, coloured according to domains, view
down the five-fold axis (a) and a side view (b) slightly tilted
to show the depth of the crater. Note the grey stem segment
leading to the C terminus of the fragment, indicated by arrows.
c, d, Micrographs of negatively stained rosettes of E1* trimers
obtained by dialysing away the detergent used for
solubilization. In the right-hand panel, a star was added to
highlight the trimers present in rings of five. The three-fold
symmetry of some of the trimers is evident, especially on panel
c. e, Model for a symmetric rosette exhibiting dodecahedral
symmetry, built according to Supplementary Information. The
magnification is about three times that of the rosettes
presented in panels c and d.
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Figure 4.
Figure 4: Model for membrane fusion involving protein -protein
interactions, as explained in the text. a -d, White stars
denote hydrophilic residues and C-terminal charge in the
cytosolic tail of the fusion protein. White cylinders denote
transmembrane anchors. Broken white lines indicate the stem
region, which connects the ectodomain to the TM segments. For
clarity, the complete ring of five trimers is not shown.
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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 #3
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Title
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Structure and interactions at the viral surface of the envelope protein e1 of semliki forest virus.
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Authors
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A.Roussel,
J.Lescar,
M.C.Vaney,
G.Wengler,
G.Wengler,
F.A.Rey.
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Ref.
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Structure, 2006,
14,
75-86.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Structure of SFV E1
(A) Ribbon diagram
colored according to domains, by using the standard class II
color coding (red, yellow, and blue for DI, DII, and DIII,
respectively), except that DII is colored yellow and orange to
distinguish the two insertions into DI loops (at D[0]E[0] and
H[0]I[0]) that make up this domain, and the fusion peptide is
brown. The SS bonds are drawn as green cylinders and are labeled
from 1 to 8. A yellow fan denotes the single glycosylation site
at position 141. All of the histidine side chains present in the
structure are drawn in magenta and labeled; conserved ones are
framed (note the cluster of three histidines at the DI/DIII
interface, around His331). The side chains of mutants that
affect the lipid dependence of the fusion activity of E1 are
drawn and labeled in black. Numbered gray arrows point to the
location of E1 insertions in the more distant fish alphaviruses
(see [C]).
(B) Topological diagram of E1, drawn with TOPS
(Flores et al., 1994) and colored according to domains. The
domains are labeled in colored font (matching the class II
scheme). In DII, the central and connecting b sheets and the
fusion loop-bearing b sandwich (FLBS) are labeled in black.
(C) Amino acid sequence alignment of E1 proteins from
representative alphaviruses: Ross river virus (RRV),
O'nyong-nyong virus (NYO), Venezuelan equine encephalitis virus
(VEE), western equine encephalitis virus (WEE), Sindbis virus
(SIN), and rainbow trout sleeping disease virus (SDV). The
secondary structure is represented above the sequence, colored
coded as in (A) and (B). Highly and relatively conserved
residues are drawn in white font on red background and vice
versa, respectively, with variable positions in black. The
glycosylation site is marked by a yellow fan as in (A).
Cysteines are labeled in green with the number of the disulfide
bridge that they form (1-8, as in [A]). Insertions in the amino
acid sequence of E1 from the fish alphaviruses (SDV) are
numbered in gray to match the arrows in (A). Other symbols
underneath the alignment show E1/E1 (triangles) and E1/E2 (blue
stars) contacts on the virus particle, determined as indicated
in the Experimental Procedures. Yellow triangles denote E1/E1
contacts about the I5 and Q6 axes (Figure 2), and white
triangles denote contacts about the Q2 axes. A vertical open
arrow above the sequence marks the last amino acid with visible
electron density in the crystal (K384). The C-terminal TM region
is boxed.
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The above figure is
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #4
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Title
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Structure of a flavivirus envelope glycoprotein in its low-Ph-Induced membrane fusion conformation.
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Authors
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S.Bressanelli,
K.Stiasny,
S.L.Allison,
E.A.Stura,
S.Duquerroy,
J.Lescar,
F.X.Heinz,
F.A.Rey.
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Ref.
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EMBO J, 2004,
23,
728-738.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 Conformational rearrangement of protein E. Comparison
of the overall organization of the protein in the neutral- and
acid-pH forms. The 'top' and 'side' views are indicated in the
top and bottom rows, respectively. The three domains of sE are
labeled dI, dII, and dIII. The color coding is defined in the
legend to Figure 1. (A) Neutral -pH, dimeric conformation of sE
in a surface representation. The carbohydrate residues (labeled
CHO) are indicated in pink. A ribbon diagram is intercalated
between the top and side views, at the same scale and
orientation as the foreground subunit in the side view. Several
 -sheets
that are referred to in the text are indicated (i.e., the top
and bottom -sheets
of dI, the klD[0] and gfeah sheets of dII). In the ribbon
diagram, the arrows representing the -strands
in the bottom sheet of dI are white. The last amino acid
observed in the crystal structure (K395; Rey et al, 1995) is
indicated by an open blue star, labeled C-term. The lipid
bilayer is diagrammed at the same scale underneath the dimer in
the side view, with the aliphatic region in pale yellow and the
lipid head regions in gray. (B) Low-pH conformation of sE. As in
panel A, only one subunit is colored and the others are shown in
white and gray. The arrows show the dimensions of the molecule,
including all atoms with a Van der Waals radius of 2 Å. In the
side view, the purple region indicates the dIII/stem linker,
which ends at the last amino acid visible in the electron
density map (R401) indicated by an open red star (labeled
C-ter). Note the vertical groove that follows the C-terminus
along the interface between neighboring dIIs in the trimer. The
lipid bilayer is diagrammed as in (A), indicating the postulated
interaction of the fusion peptide loops with the lipid heads.
(C) Ribbon diagram of the polypeptide chain of sE in the
trimeric conformation. In the top view, note the extended
conformation of the dI/dIII linker (purple). In the side view,
only the colored subunit displayed in (B) is shown for clarity.
The disordered segments (the E[0]F[0] loop in dI and the fg loop
in dII) are indicated by broken lines and labeled. The
C-terminus is indicated as in (B). It shows that the predicted
 -helix
H1 of the stem would interact with the two short helices of dII.
(D) Conformational rearrangement of sE. dI of the sE subunit in
the conformation observed in the dimer (Figure 1A) was
superposed on dI of the colored subunit in the trimer shown in
(C), as explained in the text. Curved gray arrows show the
movement of the domains to reach the conformation indicated in
(C). In the side view, the two -sheets
of dII that change their relative orientation are labeled
(klD[0] and gfeah).
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Figure 6.
Figure 6 Diagram of the full-length E protein in its different
conformations. Organization of the flavivirus E protein in three
conformations: on the mature viral particle, in its postfusion
form, and in the asymmetric, low-pH-induced intermediate
conformation, responsible for the hemifusion step. The linear
diagram at the top summarizes the arrangement of domains
polypeptide segments, defining the color code used in (A, B).
(A) Cartoon of TBEV E as lying on the viral membrane at neutral
pH, as observed in the dengue virus particles (Zhang et al,
2003a) (left panel), and in its final, postfusion conformation
change (right panel). (B) Proposed structural intermediate
responsible for causing fusion of the outer leaflets of the
target and viral membranes (hemifusion step). Helix H1 maintains
the tips of dII in an open conformation, allowing two-fold
related lateral interaction between adjacent trimers via the
fusion peptide loops. This arrangement leads to the formation of
a ring of five trimers, each interacting identically with its
neighbors, which destabilizes the target membrane by creating a
lipid nipple. We propose that the H2 segment of the polypeptide
chain is used to accommodate the temporary symmetry violation
during this intermediate, acting as a tether to the TM segments.
Zipping up of the H2 (or s2 segment in SFV) will force
juxtaposition of the fusion peptide loops and the TM segments,
forcing the opening of an initial fusion pore, as proposed for
SFV E1 (Gibbons et al, 2004). For clarity, only two trimers are
drawn (out of five proposed to form a closed ring).
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by Macmillan Publishers Ltd
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