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PDBsum entry 1a6c
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* Residue conservation analysis
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DOI no:
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Structure
6:157-171
(1998)
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PubMed id:
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The structure of tobacco ringspot virus: a link in the evolution of icosahedral capsids in the picornavirus superfamily.
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V.Chandrasekar,
J.E.Johnson.
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ABSTRACT
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BACKGROUND: Tobacco ringspot virus (TRSV) is a member of the nepovirus genus of
icosahedral RNA plant viruses that cause disease in fruit crops. Nepoviruses,
comoviruses and picornaviruses are classified in the picornavirus superfamily.
Crystal structures of comoviruses and picornaviruses and the molecular mass of
the TRSV subunit (sufficient to accommodate three beta-barrel domains) suggested
that nepoviruses may represent a link in the evolution of the picornavirus
capsids from a T = 3 icosahedral virus. This evolutionary process is thought to
involve triplication of the capsid protein gene, to encode a three-domain
polyprotein, followed by development of cleavage sites in the interdomain
linking regions. Structural studies on TRSV were initiated to determine if the
TRSV subunit corresponds to the proposed uncleaved three-domain polyprotein.
RESULTS: The 3.5 A resolution structure of TRSV shows that the capsid protein
consists of three beta-barrel domains covalently linked by extended
polypeptides. The order of connectivity of the domains in TRSV confirms the
proposed connectivity for the precleaved comovirus and picornavirus capsid
polyprotein. Structural differences between equivalent domains in TRSV and
comoviruses are confined to the external surface loops, interdomain connecting
polypeptides and N termini. The three different domains within TRSV and
comoviruses are more closely related at the structural level than the three
individual domains within picornaviruses. CONCLUSIONS: The structural results
confirm the notion of divergent evolution of the capsid polyproteins of
nepoviruses, comoviruses and picornaviruses from a common ancestor. A number of
residues were found to be conserved among various nepoviruses, some of which
stabilize the quaternary structure of the three domains in the TRSV capsid
protein subunit. Two conserved regions were identified on the external surface
of TRSV, however, mutational studies will be needed to understand their
functional significance. Nepoviruses transmitted by the same nematode species do
not share regions with similar amino acid composition on the viral surface.
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Selected figure(s)
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Figure 4.
Figure 4. Interdomain linking polypeptides in TRSV, (a)
Stereo view of the Ca trace (white) of the capsid protein from
inside the capsid with the electron density for the two
domain-linking polypeptides. The pink density shows the link
between the C and B domains and the brown density shows the link
between the B and A domains. (b) An enlarged view of (a) showing
the difference in the conformation of the C-B domain-connecting
polypeptides in TRSV (yellow) and BPMV (green).
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1998,
6,
157-171)
copyright 1998.
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Figure was
selected
by an automated process.
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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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P.Schellenberger,
G.Demangeat,
O.Lemaire,
C.Ritzenthaler,
M.Bergdoll,
V.Oliéric,
C.Sauter,
and
B.Lorber
(2011).
Strategies for the crystallization of viruses: Using phase diagrams and gels to produce 3D crystals of Grapevine fanleaf virus.
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J Struct Biol,
174,
344-351.
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P.Schellenberger,
P.Andret-Link,
C.Schmitt-Keichinger,
M.Bergdoll,
A.Marmonier,
E.Vigne,
O.Lemaire,
M.Fuchs,
G.Demangeat,
and
C.Ritzenthaler
(2010).
A stretch of 11 amino acids in the betaB-betaC loop of the coat protein of grapevine fanleaf virus is essential for transmission by the nematode Xiphinema index.
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J Virol,
84,
7924-7933.
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A.Cheng,
J.A.Speir,
Y.A.Yuan,
J.E.Johnson,
and
S.M.Wong
(2009).
Preliminary X-ray data analysis of crystalline hibiscus chlorotic ringspot virus.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
589-593.
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H.Sanfaçon,
J.Wellink,
O.Le Gall,
A.Karasev,
R.van der Vlugt,
and
T.Wetzel
(2009).
Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus.
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Arch Virol,
154,
899-907.
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K.J.Koudelka,
G.Destito,
E.M.Plummer,
S.A.Trauger,
G.Siuzdak,
and
M.Manchester
(2009).
Endothelial targeting of cowpea mosaic virus (CPMV) via surface vimentin.
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PLoS Pathog,
5,
e1000417.
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O.Le Gall,
P.Christian,
C.M.Fauquet,
A.M.King,
N.J.Knowles,
N.Nakashima,
G.Stanway,
and
A.E.Gorbalenya
(2008).
Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture.
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Arch Virol,
153,
715-727.
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E.Estrada
(2007).
Point scattering: a new geometric invariant with applications from (nano)clusters to biomolecules.
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J Comput Chem,
28,
767-777.
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C.Zubieta,
G.Schoehn,
J.Chroboczek,
and
S.Cusack
(2005).
The structure of the human adenovirus 2 penton.
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Mol Cell,
17,
121-135.
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PDB codes:
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A.Andreeva,
D.Howorth,
S.E.Brenner,
T.J.Hubbard,
C.Chothia,
and
A.G.Murzin
(2004).
SCOP database in 2004: refinements integrate structure and sequence family data.
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Nucleic Acids Res,
32,
D226-D229.
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A.Stocker,
T.Tomizaki,
C.Schulze-Briese,
and
U.Baumann
(2002).
Crystal structure of the human supernatant protein factor.
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Structure,
10,
1533-1540.
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PDB code:
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K.Tars,
K.Fridborg,
M.Bundule,
and
L.Liljas
(2000).
Structure determination of bacteriophage PP7 from Pseudomonas aeruginosa: from poor data to a good map.
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Acta Crystallogr D Biol Crystallogr,
56,
398-405.
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PDB code:
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L.Liljas
(1999).
Virus assembly.
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Curr Opin Struct Biol,
9,
129-134.
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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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