 |
PDBsum entry 1m1c
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Nat Struct Biol
9:725-728
(2002)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
L-A virus at 3.4 A resolution reveals particle architecture and mRNA decapping mechanism.
|
|
H.Naitow,
J.Tang,
M.Canady,
R.B.Wickner,
J.E.Johnson.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The structure of the yeast L-A virus was determined by X-ray crystallography at
3.4 A resolution. The L-A dsRNA virus is 400 A in diameter and contains a single
protein shell of 60 asymmetric dimers of the coat protein, a feature common
among the inner protein shells of dsRNA viruses and probably related to their
unique mode of transcription and replication. The two identical subunits in each
dimer are in non-equivalent environments and show substantially different
conformations in specific surface regions. The L-A virus decaps cellular mRNA to
efficiently translate its own uncapped mRNA. Our structure reveals a trench at
the active site of the decapping reaction and suggests a role for nearby
residues in the reaction.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 2.
Figure 2. A region of the electron density map is shown fit with
residues 106 -114 (Ser-His-Ala-Tyr-Asn-Ile-Thr-Ser-Trp).
|
|
Figure 4.
Figure 4. A stereo view close-up of the trench showing residue
His 154 and its neighboring residues around the active site.
Residues Tyr 150, His 151, Asp 152, Tyr 452, Tyr 538 and Asp 540
all may contribute to the mRNA decapping reaction. The four
loops corresponding to loop 1, 2, 3 and 4, are colored in red,
green, blue and pink, respectively.
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2002,
9,
725-728)
copyright 2002.
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
D.Luque,
J.M.González,
D.Garriga,
S.A.Ghabrial,
W.M.Havens,
B.Trus,
N.Verdaguer,
J.L.Carrascosa,
and
J.R.Castón
(2010).
The T=1 capsid protein of Penicillium chrysogenum virus is formed by a repeated helix-rich core indicative of gene duplication.
|
| |
J Virol,
84,
7256-7266.
|
|
|
|
|
|
|
E.V.Koonin
(2010).
Taming of the shrewd: novel eukaryotic genes from RNA viruses.
|
| |
BMC Biol,
8,
2.
|
|
|
|
|
|
|
L.Cheng,
J.Zhu,
W.H.Hui,
X.Zhang,
B.Honig,
Q.Fang,
and
Z.H.Zhou
(2010).
Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics.
|
| |
J Mol Biol,
397,
852-863.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Y.J.Tao,
and
Q.Ye
(2010).
RNA virus replication complexes.
|
| |
PLoS Pathog,
6,
e1000943.
|
|
|
|
|
|
|
D.J.Taylor,
and
J.Bruenn
(2009).
The evolution of novel fungal genes from non-retroviral RNA viruses.
|
| |
BMC Biol,
7,
88.
|
|
|
|
|
|
|
J.Pan,
L.Dong,
L.Lin,
W.F.Ochoa,
R.S.Sinkovits,
W.M.Havens,
M.L.Nibert,
T.S.Baker,
S.A.Ghabrial,
and
Y.J.Tao
(2009).
Atomic structure reveals the unique capsid organization of a dsRNA virus.
|
| |
Proc Natl Acad Sci U S A,
106,
4225-4230.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Jalasvuori,
S.T.Jaatinen,
S.Laurinavicius,
E.Ahola-Iivarinen,
N.Kalkkinen,
D.H.Bamford,
and
J.K.Bamford
(2009).
The closest relatives of icosahedral viruses of thermophilic bacteria are among viruses and plasmids of the halophilic archaea.
|
| |
J Virol,
83,
9388-9397.
|
|
|
|
|
|
|
S.A.Ghabrial,
and
M.L.Nibert
(2009).
Victorivirus, a new genus of fungal viruses in the family Totiviridae.
|
| |
Arch Virol,
154,
373-379.
|
|
|
|
|
|
|
S.A.Ghabrial,
and
N.Suzuki
(2009).
Viruses of plant pathogenic fungi.
|
| |
Annu Rev Phytopathol,
47,
353-384.
|
|
|
|
|
|
|
S.B.Rochal,
and
V.L.Lorman
(2009).
Theory of a reconstructive structural transformation in capsids of icosahedral viruses.
|
| |
Phys Rev E Stat Nonlin Soft Matter Phys,
80,
051905.
|
|
|
|
|
|
|
S.Duquerroy,
B.Da Costa,
C.Henry,
A.Vigouroux,
S.Libersou,
J.Lepault,
J.Navaza,
B.Delmas,
and
F.A.Rey
(2009).
The picobirnavirus crystal structure provides functional insights into virion assembly and cell entry.
|
| |
EMBO J,
28,
1655-1665.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.Gunawardana,
H.C.Cheng,
and
K.R.Gayler
(2008).
Identification of functional domains in Arabidopsis thaliana mRNA decapping enzyme (AtDcp2).
|
| |
Nucleic Acids Res,
36,
203-216.
|
|
|
|
|
|
|
J.E.Johnson
(2008).
Multi-disciplinary studies of viruses: the role of structure in shaping the questions and answers.
|
| |
J Struct Biol,
163,
246-253.
|
|
|
|
|
|
|
J.Tang,
W.F.Ochoa,
R.S.Sinkovits,
B.T.Poulos,
S.A.Ghabrial,
D.V.Lightner,
T.S.Baker,
and
M.L.Nibert
(2008).
Infectious myonecrosis virus has a totivirus-like, 120-subunit capsid, but with fiber complexes at the fivefold axes.
|
| |
Proc Natl Acad Sci U S A,
105,
17526-17531.
|
|
|
|
|
|
|
N.Miyazaki,
T.Uehara-Ichiki,
L.Xing,
L.Bergman,
A.Higashiura,
A.Nakagawa,
T.Omura,
and
R.H.Cheng
(2008).
Structural evolution of reoviridae revealed by oryzavirus in acquiring the second capsid shell.
|
| |
J Virol,
82,
11344-11353.
|
|
|
|
|
|
|
W.F.Ochoa,
W.M.Havens,
R.S.Sinkovits,
M.L.Nibert,
S.A.Ghabrial,
and
T.S.Baker
(2008).
Partitivirus structure reveals a 120-subunit, helix-rich capsid with distinctive surface arches formed by quasisymmetric coat-protein dimers.
|
| |
Structure,
16,
776-786.
|
|
|
|
|
|
|
F.Powilleit,
T.Breinig,
and
M.J.Schmitt
(2007).
Exploiting the yeast L-A viral capsid for the in vivo assembly of chimeric VLPs as platform in vaccine development and foreign protein expression.
|
| |
PLoS ONE,
2,
e415.
|
|
|
|
|
|
|
H.T.Jäälinoja,
J.T.Huiskonen,
and
S.J.Butcher
(2007).
Electron cryomicroscopy comparison of the architectures of the enveloped bacteriophages phi6 and phi8.
|
| |
Structure,
15,
157-167.
|
|
|
|
|
|
|
V.L.Lorman,
and
S.B.Rochal
(2007).
Density-wave theory of the capsid structure of small icosahedral viruses.
|
| |
Phys Rev Lett,
98,
185502.
|
|
|
|
|
|
|
C.R.Bourne,
M.G.Finn,
and
A.Zlotnick
(2006).
Global structural changes in hepatitis B virus capsids induced by the assembly effector HAP1.
|
| |
J Virol,
80,
11055-11061.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.T.Huiskonen,
F.de Haas,
D.Bubeck,
D.H.Bamford,
S.D.Fuller,
and
S.J.Butcher
(2006).
Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging.
|
| |
Structure,
14,
1039-1048.
|
|
|
|
|
|
|
M.J.Schmitt,
and
F.Breinig
(2006).
Yeast viral killer toxins: lethality and self-protection.
|
| |
Nat Rev Microbiol,
4,
212-221.
|
|
|
|
|
|
|
A.Zlotnick
(2005).
Theoretical aspects of virus capsid assembly.
|
| |
J Mol Recognit,
18,
479-490.
|
|
|
|
|
|
|
C.A.Kerfeld,
M.R.Sawaya,
S.Tanaka,
C.V.Nguyen,
M.Phillips,
M.Beeby,
and
T.O.Yeates
(2005).
Protein structures forming the shell of primitive bacterial organelles.
|
| |
Science,
309,
936-938.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
C.M.Shepherd,
and
V.S.Reddy
(2005).
Extent of protein-protein interactions and quasi-equivalence in viral capsids.
|
| |
Proteins,
58,
472-477.
|
|
|
|
|
|
|
F.Coulibaly,
C.Chevalier,
I.Gutsche,
J.Pous,
J.Navaza,
S.Bressanelli,
B.Delmas,
and
F.A.Rey
(2005).
The birnavirus crystal structure reveals structural relationships among icosahedral viruses.
|
| |
Cell,
120,
761-772.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Tang,
H.Naitow,
N.A.Gardner,
A.Kolesar,
L.Tang,
R.B.Wickner,
and
J.E.Johnson
(2005).
The structural basis of recognition and removal of cellular mRNA 7-methyl G 'caps' by a viral capsid protein: a unique viral response to host defense.
|
| |
J Mol Recognit,
18,
158-168.
|
|
|
|
|
|
|
P.Ahlquist
(2005).
Virus evolution: fitting lifestyles to a T.
|
| |
Curr Biol,
15,
R465-R467.
|
|
|
|
|
|
|
W.Jiang,
and
S.J.Ludtke
(2005).
Electron cryomicroscopy of single particles at subnanometer resolution.
|
| |
Curr Opin Struct Biol,
15,
571-577.
|
|
|
|
|
|
|
E.L.Nason,
R.Rothagel,
S.K.Mukherjee,
A.K.Kar,
M.Forzan,
B.V.Prasad,
and
P.Roy
(2004).
Interactions between the inner and outer capsids of bluetongue virus.
|
| |
J Virol,
78,
8059-8067.
|
|
|
|
|
|
|
J.L.Chong,
R.Y.Chuang,
L.Tung,
and
T.H.Chang
(2004).
Ded1p, a conserved DExD/H-box translation factor, can promote yeast L-A virus negative-strand RNA synthesis in vitro.
|
| |
Nucleic Acids Res,
32,
2031-2038.
|
|
|
|
|
|
|
N.Cougot,
E.van Dijk,
S.Babajko,
and
B.Séraphin
(2004).
'Cap-tabolism'.
|
| |
Trends Biochem Sci,
29,
436-444.
|
|
|
|
|
|
|
X.Qiao,
J.Qiao,
and
L.Mindich
(2003).
Analysis of specific binding involved in genomic packaging of the double-stranded-RNA bacteriophage phi6.
|
| |
J Bacteriol,
185,
6409-6414.
|
|
|
|
|
|
|
K.M.Reinisch
(2002).
The dsRNA Viridae and their catalytic capsids.
|
| |
Nat Struct Biol,
9,
714-716.
|
|
|
|
|
|
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
code is
shown on the right.
|
|
Links
