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Contents |
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151 a.a.
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(+ 2 more)
28 a.a.*
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369 a.a.
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* Residue conservation analysis
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* C-alpha coords only
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PDB id:
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Virus
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Title:
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Placement of the structural proteins in sindbis virus
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Structure:
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Coat protein c. Chain: a, b, c, d. Synonym: capsid protein c. General control protein gcn4. Chain: e, f, g, h, i, j, k, l. Fragment: leucine-zipper (residues 225-281). Synonym: amino acid biosynthesis regulatory protein. Spike glycoprotein e1. Chain: m, n, o, p.
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Source:
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Sindbis virus. Organism_taxid: 11034. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organism_taxid: 11034
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Authors:
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W.Zhang,S.Mukhopadhyay,S.V.Pletnev,T.S.Baker,R.J.Kuhn,M.G.Rossmann
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Key ref:
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W.Zhang
et al.
(2002).
Placement of the structural proteins in Sindbis virus.
J Virol,
76,
11645-11658.
PubMed id:
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Date:
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08-Apr-02
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Release date:
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04-Nov-02
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PROCHECK
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Headers
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References
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P03316
(POLS_SINDV) -
Structural polyprotein from Sindbis virus
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Seq:
Struc:
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1245 a.a.
151 a.a.
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Enzyme class:
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Chains A, B, C, D, M, N, O, P:
E.C.3.4.21.90
- togavirin.
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Reaction:
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Autocatalytic release of the core protein from the N-terminus of the togavirus structural protein by hydrolysis of a Trp-|-Ser bond.
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J Virol
76:11645-11658
(2002)
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PubMed id:
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Placement of the structural proteins in Sindbis virus.
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W.Zhang,
S.Mukhopadhyay,
S.V.Pletnev,
T.S.Baker,
R.J.Kuhn,
M.G.Rossmann.
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ABSTRACT
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The structure of the lipid-enveloped Sindbis virus has been determined by
fitting atomic resolution crystallographic structures of component proteins into
an 11-A resolution cryoelectron microscopy map. The virus has T=4 quasisymmetry
elements that are accurately maintained between the external glycoproteins, the
transmembrane helical region, and the internal nucleocapsid core. The crystal
structure of the E1 glycoprotein was fitted into the cryoelectron microscopy
density, in part by using the known carbohydrate positions as restraints. A
difference map showed that the E2 glycoprotein was shaped similarly to E1,
suggesting a possible common evolutionary origin for these two glycoproteins.
The structure shows that the E2 glycoprotein would have to move away from the
center of the trimeric spike in order to expose enough viral membrane surface to
permit fusion with the cellular membrane during the initial stages of host
infection. The well-resolved E1-E2 transmembrane regions form alpha-helical
coiled coils that were consistent with T=4 symmetry. The known structure of the
capsid protein was fitted into the density corresponding to the nucleocapsid,
revising the structure published earlier.
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Literature references that cite this PDB file's key reference
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| |
PubMed id
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Reference
|
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|
|
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A.Zlotnick,
and
S.Mukhopadhyay
(2011).
Virus assembly, allostery and antivirals.
|
| |
Trends Microbiol,
19,
14-23.
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|
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A.Mitra,
B.Deutsch,
F.Ignatovich,
C.Dykes,
and
L.Novotny
(2010).
Nano-optofluidic detection of single viruses and nanoparticles.
|
| |
ACS Nano,
4,
1305-1312.
|
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|
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|
|
A.R.Hunt,
S.Frederickson,
T.Maruyama,
J.T.Roehrig,
and
C.D.Blair
(2010).
The first human epitope map of the alphaviral E1 and E2 proteins reveals a new E2 epitope with significant virus neutralizing activity.
|
| |
PLoS Negl Trop Dis,
4,
e739.
|
|
|
|
|
|
|
D.E.Griffin
(2010).
Recovery from viral encephalomyelitis: immune-mediated noncytolytic virus clearance from neurons.
|
| |
Immunol Res,
47,
123-133.
|
|
|
|
|
|
|
K.Morizono,
A.Ku,
Y.Xie,
A.Harui,
S.K.Kung,
M.D.Roth,
B.Lee,
and
I.S.Chen
(2010).
Redirecting lentiviral vectors pseudotyped with sindbis virus-derived envelope proteins to DC-SIGN by modification of N-linked glycans of envelope proteins.
|
| |
J Virol,
84,
6923-6934.
|
|
|
|
|
|
|
L.He,
A.Piper,
F.Meilleur,
D.A.Myles,
R.Hernandez,
D.T.Brown,
and
W.T.Heller
(2010).
The structure of Sindbis virus produced from vertebrate and invertebrate hosts as determined by small-angle neutron scattering.
|
| |
J Virol,
84,
5270-5276.
|
|
|
|
|
|
|
L.Li,
J.Jose,
Y.Xiang,
R.J.Kuhn,
and
M.G.Rossmann
(2010).
Structural changes of envelope proteins during alphavirus fusion.
|
| |
Nature,
468,
705-708.
|
|
|
PDB codes:
|
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|
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M.B.Sherman,
and
S.C.Weaver
(2010).
Structure of the recombinant alphavirus Western equine encephalitis virus revealed by cryoelectron microscopy.
|
| |
J Virol,
84,
9775-9782.
|
|
|
|
|
|
|
M.Kielian,
C.Chanel-Vos,
and
M.Liao
(2010).
Alphavirus Entry and Membrane Fusion.
|
| |
Viruses,
2,
796-825.
|
|
|
|
|
|
|
W.Akahata,
Z.Y.Yang,
H.Andersen,
S.Sun,
H.A.Holdaway,
W.P.Kong,
M.G.Lewis,
S.Higgs,
M.G.Rossmann,
S.Rao,
and
G.J.Nabel
(2010).
A virus-like particle vaccine for epidemic Chikungunya virus protects nonhuman primates against infection.
|
| |
Nat Med,
16,
334-338.
|
|
|
|
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|
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C.Sánchez-San Martín,
C.Y.Liu,
and
M.Kielian
(2009).
Dealing with low pH: entry and exit of alphaviruses and flaviviruses.
|
| |
Trends Microbiol,
17,
514-521.
|
|
|
|
|
|
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J.Jose,
J.E.Snyder,
and
R.J.Kuhn
(2009).
A structural and functional perspective of alphavirus replication and assembly.
|
| |
Future Microbiol,
4,
837-856.
|
|
|
|
|
|
|
K.X.Zhang,
M.Moussavi,
C.Kim,
E.Chow,
I.S.Chen,
L.Fazli,
W.Jia,
and
P.S.Rennie
(2009).
Lentiviruses with trastuzumab bound to their envelopes can target and kill prostate cancer cells.
|
| |
Cancer Gene Ther,
16,
820-831.
|
|
|
|
|
|
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M.M.Parrott,
S.A.Sitarski,
R.J.Arnold,
L.K.Picton,
R.B.Hill,
and
S.Mukhopadhyay
(2009).
Role of conserved cysteines in the alphavirus E3 protein.
|
| |
J Virol,
83,
2584-2591.
|
|
|
|
|
|
|
P.Schlick,
C.Taucher,
B.Schittl,
J.L.Tran,
R.M.Kofler,
W.Schueler,
A.von Gabain,
A.Meinke,
and
C.W.Mandl
(2009).
Helices alpha2 and alpha3 of West Nile virus capsid protein are dispensable for assembly of infectious virions.
|
| |
J Virol,
83,
5581-5591.
|
|
|
|
|
|
|
R.Hernandez,
and
A.Paredes
(2009).
Sindbis virus as a model for studies of conformational changes in a metastable virus and the role of conformational changes in in vitro antibody neutralisation.
|
| |
Rev Med Virol,
19,
257-272.
|
|
|
|
|
|
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R.L.Knight,
K.L.Schultz,
R.J.Kent,
M.Venkatesan,
and
D.E.Griffin
(2009).
Role of N-linked glycosylation for sindbis virus infection and replication in vertebrate and invertebrate systems.
|
| |
J Virol,
83,
5640-5647.
|
|
|
|
|
|
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W.Thongthai,
and
K.Weninger
(2009).
Photoinactivation of sindbis virus infectivity without inhibition of membrane fusion.
|
| |
Photochem Photobiol,
85,
801-806.
|
|
|
|
|
|
|
Z.L.Qin,
Y.Zheng,
and
M.Kielian
(2009).
Role of conserved histidine residues in the low-pH dependence of the Semliki Forest virus fusion protein.
|
| |
J Virol,
83,
4670-4677.
|
|
|
|
|
|
|
A.Siber,
and
R.Podgornik
(2008).
Nonspecific interactions in spontaneous assembly of empty versus functional single-stranded RNA viruses.
|
| |
Phys Rev E Stat Nonlin Soft Matter Phys,
78,
051915.
|
|
|
|
|
|
|
C.L.Murray,
J.Marcotrigiano,
and
C.M.Rice
(2008).
Bovine viral diarrhea virus core is an intrinsically disordered protein that binds RNA.
|
| |
J Virol,
82,
1294-1304.
|
|
|
|
|
|
|
D.J.Pierro,
E.L.Powers,
and
K.E.Olson
(2008).
Genetic determinants of Sindbis virus mosquito infection are associated with a highly conserved alphavirus and flavivirus envelope sequence.
|
| |
J Virol,
82,
2966-2974.
|
|
|
|
|
|
|
G.Vestergaard,
R.Aramayo,
T.Basta,
M.Häring,
X.Peng,
K.Brügger,
L.Chen,
R.Rachel,
N.Boisset,
R.A.Garrett,
and
D.Prangishvili
(2008).
Structure of the acidianus filamentous virus 3 and comparative genomics of related archaeal lipothrixviruses.
|
| |
J Virol,
82,
371-381.
|
|
|
|
|
|
|
R.Hernandez,
A.Paredes,
and
D.T.Brown
(2008).
Sindbis virus conformational changes induced by a neutralizing anti-E1 monoclonal antibody.
|
| |
J Virol,
82,
5750-5760.
|
|
|
|
|
|
|
R.Warrier,
B.R.Linger,
B.L.Golden,
and
R.J.Kuhn
(2008).
Role of sindbis virus capsid protein region II in nucleocapsid core assembly and encapsidation of genomic RNA.
|
| |
J Virol,
82,
4461-4470.
|
|
|
|
|
|
|
C.K.Navaratnarajah,
and
R.J.Kuhn
(2007).
Functional characterization of the Sindbis virus E2 glycoprotein by transposon linker-insertion mutagenesis.
|
| |
Virology,
363,
134-147.
|
|
|
|
|
|
|
E.Falkowska,
F.Kajumo,
E.Garcia,
J.Reinus,
and
T.Dragic
(2007).
Hepatitis C virus envelope glycoprotein E2 glycans modulate entry, CD81 binding, and neutralization.
|
| |
J Virol,
81,
8072-8079.
|
|
|
|
|
|
|
E.Teissier,
and
E.I.Pécheur
(2007).
Lipids as modulators of membrane fusion mediated by viral fusion proteins.
|
| |
Eur Biophys J,
36,
887-899.
|
|
|
|
|
|
|
M.L.Plassmeyer,
S.S.Soldan,
K.M.Stachelek,
S.M.Roth,
J.Martín-García,
and
F.González-Scarano
(2007).
Mutagenesis of the La Crosse Virus glycoprotein supports a role for Gc (1066-1087) as the fusion peptide.
|
| |
Virology,
358,
273-282.
|
|
|
|
|
|
|
X.Yan,
K.A.Dryden,
J.Tang,
and
T.S.Baker
(2007).
Ab initio random model method facilitates 3D reconstruction of icosahedral particles.
|
| |
J Struct Biol,
157,
211-225.
|
|
|
|
|
|
|
Y.Zhang,
B.Kaufmann,
P.R.Chipman,
R.J.Kuhn,
and
M.G.Rossmann
(2007).
Structure of immature West Nile virus.
|
| |
J Virol,
81,
6141-6145.
|
|
|
PDB code:
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|
|
|
|
|
|
A.Fotin,
T.Kirchhausen,
N.Grigorieff,
S.C.Harrison,
T.Walz,
and
Y.Cheng
(2006).
Structure determination of clathrin coats to subnanometer resolution by single particle cryo-electron microscopy.
|
| |
J Struct Biol,
156,
453-460.
|
|
|
|
|
|
|
A.Roussel,
J.Lescar,
M.C.Vaney,
G.Wengler,
G.Wengler,
and
F.A.Rey
(2006).
Structure and interactions at the viral surface of the envelope protein E1 of Semliki Forest virus.
|
| |
Structure,
14,
75-86.
|
|
|
PDB code:
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|
|
|
|
|
|
C.Chanel-Vos,
and
M.Kielian
(2006).
Second-site revertants of a Semliki Forest virus fusion-block mutation reveal the dynamics of a class II membrane fusion protein.
|
| |
J Virol,
80,
6115-6122.
|
|
|
|
|
|
|
E.M.Hong,
R.Perera,
and
R.J.Kuhn
(2006).
Alphavirus capsid protein helix I controls a checkpoint in nucleocapsid core assembly.
|
| |
J Virol,
80,
8848-8855.
|
|
|
|
|
|
|
K.A.Dryden,
S.F.Wieland,
C.Whitten-Bauer,
J.L.Gerin,
F.V.Chisari,
and
M.Yeager
(2006).
Native hepatitis B virions and capsids visualized by electron cryomicroscopy.
|
| |
Mol Cell,
22,
843-850.
|
|
|
|
|
|
|
M.Kielian,
and
F.A.Rey
(2006).
Virus membrane-fusion proteins: more than one way to make a hairpin.
|
| |
Nat Rev Microbiol,
4,
67-76.
|
|
|
|
|
|
|
M.Liao,
and
M.Kielian
(2006).
Functions of the stem region of the Semliki Forest virus fusion protein during virus fusion and assembly.
|
| |
J Virol,
80,
11362-11369.
|
|
|
|
|
|
|
M.Liao,
and
M.Kielian
(2006).
Site-directed antibodies against the stem region reveal low pH-induced conformational changes of the Semliki Forest virus fusion protein.
|
| |
J Virol,
80,
9599-9607.
|
|
|
|
|
|
|
S.Mukhopadhyay,
W.Zhang,
S.Gabler,
P.R.Chipman,
E.G.Strauss,
J.H.Strauss,
T.S.Baker,
R.J.Kuhn,
and
M.G.Rossmann
(2006).
Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
|
| |
Structure,
14,
63-73.
|
|
|
PDB code:
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|
|
S.S.Negi,
A.A.Kolokoltsov,
C.H.Schein,
R.A.Davey,
and
W.Braun
(2006).
Determining functionally important amino acid residues of the E1 protein of Venezuelan equine encephalitis virus.
|
| |
J Mol Model,
12,
921-929.
|
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|
|
|
Y.Gao,
P.Whitaker-Dowling,
S.C.Watkins,
J.A.Griffin,
and
I.Bergman
(2006).
Rapid adaptation of a recombinant vesicular stomatitis virus to a targeted cell line.
|
| |
J Virol,
80,
8603-8612.
|
|
|
|
|
|
|
D.W.Beasley,
M.C.Whiteman,
S.Zhang,
C.Y.Huang,
B.S.Schneider,
D.R.Smith,
G.D.Gromowski,
S.Higgs,
R.M.Kinney,
and
A.D.Barrett
(2005).
Envelope protein glycosylation status influences mouse neuroinvasion phenotype of genetic lineage 1 West Nile virus strains.
|
| |
J Virol,
79,
8339-8347.
|
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|
|
|
|
F.Förster,
O.Medalia,
N.Zauberman,
W.Baumeister,
and
D.Fass
(2005).
Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography.
|
| |
Proc Natl Acad Sci U S A,
102,
4729-4734.
|
|
|
|
|
|
|
M.G.Rossmann,
M.C.Morais,
P.G.Leiman,
and
W.Zhang
(2005).
Combining X-ray crystallography and electron microscopy.
|
| |
Structure,
13,
355-362.
|
|
|
|
|
|
|
M.Liao,
and
M.Kielian
(2005).
Domain III from class II fusion proteins functions as a dominant-negative inhibitor of virus membrane fusion.
|
| |
J Cell Biol,
171,
111-120.
|
|
|
|
|
|
|
M.Liao,
and
M.Kielian
(2005).
The conserved glycine residues in the transmembrane domain of the Semliki Forest virus fusion protein are not required for assembly and fusion.
|
| |
Virology,
332,
430-437.
|
|
|
|
|
|
|
N.K.Krishna
(2005).
Identification of structural domains involved in astrovirus capsid biology.
|
| |
Viral Immunol,
18,
17-26.
|
|
|
|
|
|
|
R.Hernandez,
D.Ferreira,
C.Sinodis,
K.Litton,
and
D.T.Brown
(2005).
Single amino acid insertions at the junction of the sindbis virus E2 transmembrane domain and endodomain disrupt virus envelopment and alter infectivity.
|
| |
J Virol,
79,
7682-7697.
|
|
|
|
|
|
|
S.Mukhopadhyay,
R.J.Kuhn,
and
M.G.Rossmann
(2005).
A structural perspective of the flavivirus life cycle.
|
| |
Nat Rev Microbiol,
3,
13-22.
|
|
|
|
|
|
|
V.Madan,
M.A.Sanz,
and
L.Carrasco
(2005).
Requirement of the vesicular system for membrane permeabilization by Sindbis virus.
|
| |
Virology,
332,
307-315.
|
|
|
|
|
|
|
X.Zhang,
and
M.Kielian
(2005).
An interaction site of the envelope proteins of Semliki Forest virus that is preserved after proteolytic activation.
|
| |
Virology,
337,
344-352.
|
|
|
|
|
|
|
B.R.Linger,
L.Kunovska,
R.J.Kuhn,
and
B.L.Golden
(2004).
Sindbis virus nucleocapsid assembly: RNA folding promotes capsid protein dimerization.
|
| |
RNA,
10,
128-138.
|
|
|
|
|
|
|
C.Chanel-Vos,
and
M.Kielian
(2004).
A conserved histidine in the ij loop of the Semliki Forest virus E1 protein plays an important role in membrane fusion.
|
| |
J Virol,
78,
13543-13552.
|
|
|
|
|
|
|
C.E.Garry,
and
R.F.Garry
(2004).
Proteomics computational analyses suggest that the carboxyl terminal glycoproteins of Bunyaviruses are class II viral fusion protein (beta-penetrenes).
|
| |
Theor Biol Med Model,
1,
10.
|
|
|
|
|
|
|
D.L.Gibbons,
A.Ahn,
M.Liao,
L.Hammar,
R.H.Cheng,
and
M.Kielian
(2004).
Multistep regulation of membrane insertion of the fusion peptide of Semliki Forest virus.
|
| |
J Virol,
78,
3312-3318.
|
|
|
|
|
|
|
D.L.Gibbons,
B.Reilly,
A.Ahn,
M.C.Vaney,
A.Vigouroux,
F.A.Rey,
and
M.Kielian
(2004).
Purification and crystallization reveal two types of interactions of the fusion protein homotrimer of Semliki Forest virus.
|
| |
J Virol,
78,
3514-3523.
|
|
|
|
|
|
|
D.L.Gibbons,
M.C.Vaney,
A.Roussel,
A.Vigouroux,
B.Reilly,
J.Lepault,
M.Kielian,
and
F.A.Rey
(2004).
Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus.
|
| |
Nature,
427,
320-325.
|
|
|
PDB code:
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|
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|
|
S.Bressanelli,
K.Stiasny,
S.L.Allison,
E.A.Stura,
S.Duquerroy,
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F.X.Heinz,
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F.A.Rey
(2004).
Structure of a flavivirus envelope glycoprotein in its low-pH-induced membrane fusion conformation.
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EMBO J,
23,
728-738.
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PDB code:
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A.Op De Beeck,
and
J.Dubuisson
(2003).
Topology of hepatitis C virus envelope glycoproteins.
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Rev Med Virol,
13,
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K.Stiasny,
C.Koessl,
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Involvement of lipids in different steps of the flavivirus fusion mechanism.
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J Virol,
77,
7856-7862.
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L.K.Tamm,
J.Crane,
and
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(2003).
Membrane fusion: a structural perspective on the interplay of lipids and proteins.
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Curr Opin Struct Biol,
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453-466.
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M.Sjöberg,
and
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(2003).
Interactions between the transmembrane segments of the alphavirus E1 and E2 proteins play a role in virus budding and fusion.
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J Virol,
77,
3441-3450.
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R.Perera,
C.Navaratnarajah,
and
R.J.Kuhn
(2003).
A heterologous coiled coil can substitute for helix I of the Sindbis virus capsid protein.
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J Virol,
77,
8345-8353.
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W.Zhang,
P.R.Chipman,
J.Corver,
P.R.Johnson,
Y.Zhang,
S.Mukhopadhyay,
T.S.Baker,
J.H.Strauss,
M.G.Rossmann,
and
R.J.Kuhn
(2003).
Visualization of membrane protein domains by cryo-electron microscopy of dengue virus.
|
| |
Nat Struct Biol,
10,
907-912.
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|
PDB code:
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X.Zhang,
M.Fugère,
R.Day,
and
M.Kielian
(2003).
Furin processing and proteolytic activation of Semliki Forest virus.
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J Virol,
77,
2981-2989.
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Y.Zhang,
J.Corver,
P.R.Chipman,
W.Zhang,
S.V.Pletnev,
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R.J.Kuhn,
and
M.G.Rossmann
(2003).
Structures of immature flavivirus particles.
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EMBO J,
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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