|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
1284 a.a.
|
|
|
|
|
|
|
|
|
|
|
1031 a.a.
|
|
|
|
|
|
|
|
|
|
|
1221 a.a.
|
|
|
|
|
|
|
|
|
|
|
417 a.a.
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Virus
|
|
|
Title:
|
|
Reovirus core
|
|
Structure:
|
|
Lambda2. Chain: a. Lambda1. Chain: b, c. Sigma2. Chain: d, e
|
|
Source:
|
|
Reovirus sp.. Organism_taxid: 10891. Strain: reassortant f18. Strain: reassortant f18
|
|
Resolution:
|
|
|
3.60Å
|
R-factor:
|
0.206
|
R-free:
|
0.208
|
|
|
Authors:
|
|
K.M.Reinisch,M.L.Nibert,S.C.Harrison
|
Key ref:
|
|
K.M.Reinisch
et al.
(2000).
Structure of the reovirus core at 3.6 A resolution.
Nature,
404,
960-967.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
29-Feb-00
|
Release date:
|
12-Jul-00
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
P11079
(LMBD2_REOVD) -
Outer capsid protein lambda-2 from Reovirus type 3 (strain Dearing)
|
|
|
|
Seq:
Struc:
|
|
|
|
1289 a.a.
1284 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
P15024
(LMBD1_REOVD) -
Inner capsid protein lambda-1 from Reovirus type 3 (strain Dearing)
|
|
|
|
Seq:
Struc:
|
|
|
|
1275 a.a.
1031 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class 1:
|
|
Chain A:
E.C.2.1.1.56
- mRNA (guanine-N(7))-methyltransferase.
|
|
|
|
|
|
|
Reaction:
|
|
a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine
|
|
|
|
|
|
5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA
|
+
|
S-adenosyl-L- methionine
|
=
|
5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA
|
+
|
S-adenosyl-L-homocysteine
|
|
|
|
|
|
|
|
|
|
Enzyme class 2:
|
|
Chain A:
E.C.2.7.7.50
- mRNA guanylyltransferase.
|
|
|
|
|
|
|
Reaction:
|
|
a 5'-end diphospho-ribonucleoside in mRNA + GTP + H+ = a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate
|
|
|
|
|
|
5'-end diphospho-ribonucleoside in mRNA
|
+
|
GTP
|
+
|
H(+)
|
=
|
5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA
|
+
|
diphosphate
|
|
|
|
|
|
|
|
|
|
Enzyme class 3:
|
|
Chains B, C:
E.C.3.6.4.13
- Rna helicase.
|
|
|
|
|
|
|
Reaction:
|
|
ATP + H2O = ADP + phosphate + H+
|
|
|
|
|
|
ATP
|
+
|
H2O
|
=
|
ADP
|
+
|
phosphate
|
+
|
H(+)
|
|
|
|
|
|
|
|
|
|
|
|
|
Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
|
|
|
|
Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
| |
|
DOI no:
|
Nature
404:960-967
(2000)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Structure of the reovirus core at 3.6 A resolution.
|
|
K.M.Reinisch,
M.L.Nibert,
S.C.Harrison.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The reovirus core is an assembly with a relative molecular mass of 52 million
that synthesizes, modifies and exports viral messenger RNA. Analysis of its
structure by X-ray crystallography shows that there are alternative, specific
and completely non-equivalent contacts made by several surfaces of two of its
proteins; that the RNA capping and export apparatus is a hollow cylinder, which
probably sequesters its substrate to ensure completion of the capping reactions;
that the genomic double-stranded RNA is coiled into concentric layers within the
particle; and that there is a protein shell that appears to be common to all
groups of double-stranded RNA viruses.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 1.
Figure 1: The reovirus core particle, represented by C
alpha- traces
of the constituent subunits. lambda- 1
(relative molecular mass (M[r]) 142K (ref.46), 120 copies; shown
in red) forms the shell that packages RNA and defines the
symmetry and size of the particle.  2
(M[r] 47K, 150 copies; shown as yellow, green and white nodules)
stabilizes the  1
shell. 2
(M[ r] 144K, 60 copies; shown in blue) forms turret-like
structures around the fivefold axes that cap the nascent mRNA
and organize its extrusion.
|
|
Figure 6.
Figure 6: The capping complex. a, b, 2
turret (about 120 Å diameter and 80 Å tall) viewed from the top
and side, respectively. The five elongated 2
monomers, each shown in a different colour, wrap around the
outer surface, with their long axes at about 45° to the radial
direction. c, The 2
monomer, viewed from the inside of the pentamer (the blue
monomer in b). The GTase domain is red, methylase-1 is yellow,
methylase-2 is green and the immunoglobulin-like domains are
blue. Red SAH molecules mark the SAM-binding sites. d, GTase
domain at 90° to c, in graded colours with the N terminus red
and the C terminus blue. Side chains of K190 and K171 are shown.
e, Diagrams of SAM-binding domains. The 'universal' SAM-binding
domain is shown in black19, 20; methylase-1 is yellow and
methylase-2 is green. Secondary structural elements are aligned
vertically with their equivalents in the universal fold. The
SAM-binding position with respect to the  -sheet
is labelled. f, Two monomers of 2
(labelled A and B) with the immunoglobulin-like domains detached
and viewed from the interior of the turret. Monomer A includes
GTase 'a' and methylases 'a1' and 'a2'; B includes 'b', 'b1' and
'b2'. Coloured as in c. Red SAH molecules indicate SAM-binding
locations. Blue arrows indicate the GTase active site. g, SAH
density for methylase-1 in a 4 Å, 2F[o]- F[c] map made with data
from crystals soaked in 2 mM SAH. SAH binding is accompanied by
conformational changes in residues 519-524 and 579-587. Some
residues that may interact with SAH are labelled. h, SAH density
for methylase-2.
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2000,
404,
960-967)
copyright 2000.
|
|
| |
Figures were
selected
by the author.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
E.Decroly,
F.Ferron,
J.Lescar,
and
B.Canard
(2012).
Conventional and unconventional mechanisms for capping viral mRNA.
|
| |
Nat Rev Microbiol,
10,
51-65.
|
|
|
|
|
|
|
S.D.Trask,
S.M.McDonald,
and
J.T.Patton
(2012).
Structural insights into the coupling of virion assembly and rotavirus replication.
|
| |
Nat Rev Microbiol,
10,
165-177.
|
|
|
|
|
|
|
L.Cheng,
J.Sun,
K.Zhang,
Z.Mou,
X.Huang,
G.Ji,
F.Sun,
J.Zhang,
and
P.Zhu
(2011).
Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping.
|
| |
Proc Natl Acad Sci U S A,
108,
1373-1378.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
N.Grigorieff,
and
S.C.Harrison
(2011).
Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy.
|
| |
Curr Opin Struct Biol,
21,
265-273.
|
|
|
|
|
|
|
B.McClain,
E.Settembre,
B.R.Temple,
A.R.Bellamy,
and
S.C.Harrison
(2010).
X-ray crystal structure of the rotavirus inner capsid particle at 3.8 A resolution.
|
| |
J Mol Biol,
397,
587-599.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.L.Lawson
(2010).
Unified data resource for cryo-EM.
|
| |
Methods Enzymol,
483,
73-90.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
J.A.den Boon,
A.Diaz,
and
P.Ahlquist
(2010).
Cytoplasmic viral replication complexes.
|
| |
Cell Host Microbe,
8,
77-85.
|
|
|
|
|
|
|
J.Zhu,
L.Cheng,
Q.Fang,
Z.H.Zhou,
and
B.Honig
(2010).
Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement.
|
| |
J Mol Biol,
397,
835-851.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
L.J.Yap,
D.Luo,
K.Y.Chung,
S.P.Lim,
C.Bodenreider,
C.Noble,
P.Y.Shi,
and
J.Lescar
(2010).
Crystal structure of the dengue virus methyltransferase bound to a 5'-capped octameric RNA.
|
| |
PLoS One,
5,
0.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.Bouvet,
C.Debarnot,
I.Imbert,
B.Selisko,
E.J.Snijder,
B.Canard,
and
E.Decroly
(2010).
In vitro reconstitution of SARS-coronavirus mRNA cap methylation.
|
| |
PLoS Pathog,
6,
e1000863.
|
|
|
|
|
|
|
N.Miyazaki,
B.Wu,
K.Hagiwara,
C.Y.Wang,
L.Xing,
L.Hammar,
A.Higashiura,
T.Tsukihara,
A.Nakagawa,
T.Omura,
and
R.H.Cheng
(2010).
The functional organization of the internal components of Rice dwarf virus.
|
| |
J Biochem,
147,
843-850.
|
|
|
|
|
|
|
Y.J.Tao,
and
Q.Ye
(2010).
RNA virus replication complexes.
|
| |
PLoS Pathog,
6,
e1000943.
|
|
|
|
|
|
|
Z.Dauter,
M.Jaskolski,
and
A.Wlodawer
(2010).
Impact of synchrotron radiation on macromolecular crystallography: a personal view.
|
| |
J Synchrotron Radiat,
17,
433-444.
|
|
|
|
|
|
|
A.A.Demidenko,
and
M.L.Nibert
(2009).
Probing the transcription mechanisms of reovirus cores with molecules that alter RNA duplex stability.
|
| |
J Virol,
83,
5659-5670.
|
|
|
|
|
|
|
A.Korkut,
and
W.A.Hendrickson
(2009).
A force field for virtual atom molecular mechanics of proteins.
|
| |
Proc Natl Acad Sci U S A,
106,
15667-15672.
|
|
|
|
|
|
|
B.Sherry
(2009).
Rotavirus and reovirus modulation of the interferon response.
|
| |
J Interferon Cytokine Res,
29,
559-567.
|
|
|
|
|
|
|
E.B.Ludmir,
and
L.W.Enquist
(2009).
Viral genomes are part of the phylogenetic tree of life.
|
| |
Nat Rev Microbiol,
7,
615; author reply 615.
|
|
|
|
|
|
|
G.R.Nemerow,
L.Pache,
V.Reddy,
and
P.L.Stewart
(2009).
Insights into adenovirus host cell interactions from structural studies.
|
| |
Virology,
384,
380-388.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
L.Zhang,
M.A.Agosto,
T.Ivanovic,
D.S.King,
M.L.Nibert,
and
S.C.Harrison
(2009).
Requirements for the formation of membrane pores by the reovirus myristoylated micro1N peptide.
|
| |
J Virol,
83,
7004-7014.
|
|
|
|
|
|
|
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.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:
|
|
|
|
|
|
|
|
Z.Li,
M.L.Baker,
W.Jiang,
M.K.Estes,
and
B.V.Prasad
(2009).
Rotavirus architecture at subnanometer resolution.
|
| |
J Virol,
83,
1754-1766.
|
|
|
|
|
|
|
E.Decroly,
I.Imbert,
B.Coutard,
M.Bouvet,
B.Selisko,
K.Alvarez,
A.E.Gorbalenya,
E.J.Snijder,
and
B.Canard
(2008).
Coronavirus nonstructural protein 16 is a cap-0 binding enzyme possessing (nucleoside-2'O)-methyltransferase activity.
|
| |
J Virol,
82,
8071-8084.
|
|
|
|
|
|
|
H.Dong,
S.Ren,
B.Zhang,
Y.Zhou,
F.Puig-Basagoiti,
H.Li,
and
P.Y.Shi
(2008).
West Nile virus methyltransferase catalyzes two methylations of the viral RNA cap through a substrate-repositioning mechanism.
|
| |
J Virol,
82,
4295-4307.
|
|
|
|
|
|
|
H.Dong,
S.Ren,
H.Li,
and
P.Y.Shi
(2008).
Separate molecules of West Nile virus methyltransferase can independently catalyze the N7 and 2'-O methylations of viral RNA cap.
|
| |
Virology,
377,
1-6.
|
|
|
|
|
|
|
H.Kroschewski,
S.P.Lim,
R.E.Butcher,
T.L.Yap,
J.Lescar,
P.J.Wright,
S.G.Vasudevan,
and
A.D.Davidson
(2008).
Mutagenesis of the dengue virus type 2 NS5 methyltransferase domain.
|
| |
J Biol Chem,
283,
19410-19421.
|
|
|
|
|
|
|
I.I.Mendez,
S.G.Weiner,
Y.M.She,
M.Yeager,
and
K.M.Coombs
(2008).
Conformational changes accompany activation of reovirus RNA-dependent RNA transcription.
|
| |
J Struct Biol,
162,
277-289.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
L.Cheng,
Q.Fang,
S.Shah,
I.C.Atanasov,
and
Z.H.Zhou
(2008).
Subnanometer-resolution structures of the grass carp reovirus core and virion.
|
| |
J Mol Biol,
382,
213-222.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
P.Guardado-Calvo,
L.Vazquez-Iglesias,
J.Martinez-Costas,
A.L.Llamas-Saiz,
G.Schoehn,
G.C.Fox,
X.L.Hermo-Parrado,
J.Benavente,
and
M.J.van Raaij
(2008).
Crystal structure of the avian reovirus inner capsid protein sigmaA.
|
| |
J Virol,
82,
11208-11216.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
P.Roy
(2008).
Bluetongue virus: dissection of the polymerase complex.
|
| |
J Gen Virol,
89,
1789-1804.
|
|
|
|
|
|
|
S.Libersou,
X.Siebert,
M.Ouldali,
L.F.Estrozi,
J.Navaza,
A.Charpilienne,
P.Garnier,
D.Poncet,
and
J.Lepault
(2008).
Geometric mismatches within the concentric layers of rotavirus particles: a potential regulatory switch of viral particle transcription activity.
|
| |
J Virol,
82,
2844-2852.
|
|
|
|
|
|
|
S.M.McDonald,
and
J.T.Patton
(2008).
Molecular characterization of a subgroup specificity associated with the rotavirus inner capsid protein VP2.
|
| |
J Virol,
82,
2752-2764.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
X.Yu,
L.Jin,
and
Z.H.Zhou
(2008).
3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy.
|
| |
Nature,
453,
415-419.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Z.H.Zhou
(2008).
Towards atomic resolution structural determination by single-particle cryo-electron microscopy.
|
| |
Curr Opin Struct Biol,
18,
218-228.
|
|
|
|
|
|
|
B.G.Kopek,
G.Perkins,
D.J.Miller,
M.H.Ellisman,
and
P.Ahlquist
(2007).
Three-dimensional analysis of a viral RNA replication complex reveals a virus-induced mini-organelle.
|
| |
PLoS Biol,
5,
e220.
|
|
|
|
|
|
|
E.Mastrangelo,
M.Bollati,
M.Milani,
B.Selisko,
F.Peyrane,
B.Canard,
G.Grard,
X.de Lamballerie,
and
M.Bolognesi
(2007).
Structural bases for substrate recognition and activity in Meaban virus nucleoside-2'-O-methyltransferase.
|
| |
Protein Sci,
16,
1133-1145.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
G.Sutton,
J.M.Grimes,
D.I.Stuart,
and
P.Roy
(2007).
Bluetongue virus VP4 is an RNA-capping assembly line.
|
| |
Nat Struct Mol Biol,
14,
449-451.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
M.De la Peña,
O.J.Kyrieleis,
and
S.Cusack
(2007).
Structural insights into the mechanism and evolution of the vaccinia virus mRNA cap N7 methyl-transferase.
|
| |
EMBO J,
26,
4913-4925.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
T.Ogino,
and
A.K.Banerjee
(2007).
Unconventional mechanism of mRNA capping by the RNA-dependent RNA polymerase of vesicular stomatitis virus.
|
| |
Mol Cell,
25,
85-97.
|
|
|
|
|
|
|
X.L.Hermo-Parrado,
P.Guardado-Calvo,
A.L.Llamas-Saiz,
G.C.Fox,
L.Vazquez-Iglesias,
J.Martínez-Costas,
J.Benavente,
and
M.J.van Raaij
(2007).
Crystallization of the avian reovirus double-stranded RNA-binding and core protein sigmaA.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
426-429.
|
|
|
|
|
|
|
X.Tang,
J.Wu,
J.Sivaraman,
and
C.L.Hew
(2007).
Crystal structures of major envelope proteins VP26 and VP28 from white spot syndrome virus shed light on their evolutionary relationship.
|
| |
J Virol,
81,
6709-6717.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
Y.Zhou,
D.Ray,
Y.Zhao,
H.Dong,
S.Ren,
Z.Li,
Y.Guo,
K.A.Bernard,
P.Y.Shi,
and
H.Li
(2007).
Structure and function of flavivirus NS5 methyltransferase.
|
| |
J Virol,
81,
3891-3903.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.H.Brown
(2006).
Breaking symmetry in protein dimers: designs and functions.
|
| |
Protein Sci,
15,
1.
|
|
|
|
|
|
|
J.Li,
J.T.Wang,
and
S.P.Whelan
(2006).
A unique strategy for mRNA cap methylation used by vesicular stomatitis virus.
|
| |
Proc Natl Acad Sci U S A,
103,
8493-8498.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
L.Noad,
J.Shou,
K.M.Coombs,
and
R.Duncan
(2006).
Sequences of avian reovirus M1, M2 and M3 genes and predicted structure/function of the encoded mu proteins.
|
| |
Virus Res,
116,
45-57.
|
|
|
|
|
|
|
L.Zhang,
K.Chandran,
M.L.Nibert,
and
S.C.Harrison
(2006).
Reovirus mu1 structural rearrangements that mediate membrane penetration.
|
| |
J Virol,
80,
12367-12376.
|
|
|
|
|
|
|
M.S.Maginnis,
J.C.Forrest,
S.A.Kopecky-Bromberg,
S.K.Dickeson,
S.A.Santoro,
M.M.Zutter,
G.R.Nemerow,
J.M.Bergelson,
and
T.S.Dermody
(2006).
Beta1 integrin mediates internalization of mammalian reovirus.
|
| |
J Virol,
80,
2760-2770.
|
|
|
|
|
|
|
P.Ahlquist
(2006).
Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses.
|
| |
Nat Rev Microbiol,
4,
371-382.
|
|
|
|
|
|
|
B.Chen,
E.M.Vogan,
H.Gong,
J.J.Skehel,
D.C.Wiley,
and
S.C.Harrison
(2005).
Determining the structure of an unliganded and fully glycosylated SIV gp120 envelope glycoprotein.
|
| |
Structure,
13,
197-211.
|
|
|
|
|
|
|
C.Chevalier,
M.Galloux,
J.Pous,
C.Henry,
J.Denis,
B.Da Costa,
J.Navaza,
J.Lepault,
and
B.Delmas
(2005).
Structural peptides of a nonenveloped virus are involved in assembly and membrane translocation.
|
| |
J Virol,
79,
12253-12263.
|
|
|
|
|
|
|
C.M.Shepherd,
and
V.S.Reddy
(2005).
Extent of protein-protein interactions and quasi-equivalence in viral capsids.
|
| |
Proteins,
58,
472-477.
|
|
|
|
|
|
|
D.Quinkert,
R.Bartenschlager,
and
V.Lohmann
(2005).
Quantitative analysis of the hepatitis C virus replication complex.
|
| |
J Virol,
79,
13594-13605.
|
|
|
|
|
|
|
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.Li,
E.C.Fontaine-Rodriguez,
and
S.P.Whelan
(2005).
Amino acid residues within conserved domain VI of the vesicular stomatitis virus large polymerase protein essential for mRNA cap methyltransferase activity.
|
| |
J Virol,
79,
13373-13384.
|
|
|
|
|
|
|
J.Qiao,
X.Qiao,
and
L.Mindich
(2005).
In vivo studies of genomic packaging in the dsRNA bacteriophage Phi8.
|
| |
BMC Microbiol,
5,
10.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
K.L.Norman,
and
P.W.Lee
(2005).
Not all viruses are bad guys: the case for reovirus in cancer therapy.
|
| |
Drug Discov Today,
10,
847-855.
|
|
|
|
|
|
|
M.K.Yadav,
C.J.Gerdts,
R.Sanishvili,
W.W.Smith,
L.S.Roach,
R.F.Ismagilov,
P.Kuhn,
and
R.C.Stevens
(2005).
In situ data collection and structure refinement from microcapillary protein crystallization.
|
| |
J Appl Crystallogr,
38,
900-905.
|
|
|
|
|
|
|
P.Clarke,
R.L.Debiasi,
R.Goody,
C.C.Hoyt,
S.Richardson-Burns,
and
K.L.Tyler
(2005).
Mechanisms of reovirus-induced cell death and tissue injury: role of apoptosis and virus-induced perturbation of host-cell signaling and transcription factor activation.
|
| |
Viral Immunol,
18,
89.
|
|
|
|
|
|
|
V.Z.Grdzelishvili,
S.Smallwood,
D.Tower,
R.L.Hall,
D.M.Hunt,
and
S.A.Moyer
(2005).
A single amino acid change in the L-polymerase protein of vesicular stomatitis virus completely abolishes viral mRNA cap methylation.
|
| |
J Virol,
79,
7327-7337.
|
|
|
|
|
|
|
W.Jiang,
and
S.J.Ludtke
(2005).
Electron cryomicroscopy of single particles at subnanometer resolution.
|
| |
Curr Opin Struct Biol,
15,
571-577.
|
|
|
|
|
|
|
X.Zhang,
Y.Ji,
L.Zhang,
S.C.Harrison,
D.C.Marinescu,
M.L.Nibert,
and
T.S.Baker
(2005).
Features of reovirus outer capsid protein mu1 revealed by electron cryomicroscopy and image reconstruction of the virion at 7.0 Angstrom resolution.
|
| |
Structure,
13,
1545-1557.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Cavalli,
A.E.Prota,
T.Stehle,
T.S.Dermody,
M.Recanatini,
G.Folkers,
and
L.Scapozza
(2004).
A molecular dynamics study of reovirus attachment protein sigma1 reveals conformational changes in sigma1 structure.
|
| |
Biophys J,
86,
3423-3431.
|
|
|
|
|
|
|
A.L.Odegard,
K.Chandran,
X.Zhang,
J.S.Parker,
T.S.Baker,
and
M.L.Nibert
(2004).
Putative autocleavage of outer capsid protein micro1, allowing release of myristoylated peptide micro1N during particle uncoating, is critical for cell entry by reovirus.
|
| |
J Virol,
78,
8732-8745.
|
|
|
|
|
|
|
C.L.Miller,
J.S.Parker,
J.B.Dinoso,
C.D.Piggott,
M.J.Perron,
and
M.L.Nibert
(2004).
Increased ubiquitination and other covariant phenotypes attributed to a strain- and temperature-dependent defect of reovirus core protein mu2.
|
| |
J Virol,
78,
10291-10302.
|
|
|
|
|
|
|
E.J.Mancini,
D.E.Kainov,
J.M.Grimes,
R.Tuma,
D.H.Bamford,
and
D.I.Stuart
(2004).
Atomic snapshots of an RNA packaging motor reveal conformational changes linking ATP hydrolysis to RNA translocation.
|
| |
Cell,
118,
743-755.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Kim,
J.S.Parker,
K.E.Murray,
and
M.L.Nibert
(2004).
Nucleoside and RNA triphosphatase activities of orthoreovirus transcriptase cofactor mu2.
|
| |
J Biol Chem,
279,
4394-4403.
|
|
|
|
|
|
|
K.Hagiwara,
T.Higashi,
N.Miyazaki,
H.Naitow,
R.H.Cheng,
A.Nakagawa,
H.Mizuno,
T.Tsukihara,
and
T.Omura
(2004).
The amino-terminal region of major capsid protein P3 is essential for self-assembly of single-shelled core-like particles of Rice dwarf virus.
|
| |
J Virol,
78,
3145-3148.
|
|
|
|
|
|
|
L.L.Hermann,
and
K.M.Coombs
(2004).
Inhibition of reovirus by mycophenolic acid is associated with the M1 genome segment.
|
| |
J Virol,
78,
6171-6179.
|
|
|
|
|
|
|
M.L.Nibert,
and
J.Kim
(2004).
Conserved sequence motifs for nucleoside triphosphate binding unique to turreted reoviridae members and coltiviruses.
|
| |
J Virol,
78,
5528-5530.
|
|
|
|
|
|
|
S.C.Harrison
(2004).
Whither structural biology?
|
| |
Nat Struct Mol Biol,
11,
12-15.
|
|
|
|
|
|
|
T.J.Broering,
J.Kim,
C.L.Miller,
C.D.Piggott,
J.B.Dinoso,
M.L.Nibert,
and
J.S.Parker
(2004).
Reovirus nonstructural protein mu NS recruits viral core surface proteins and entering core particles to factory-like inclusions.
|
| |
J Virol,
78,
1882-1892.
|
|
|
|
|
|
|
W.Xu,
M.K.Patrick,
P.R.Hazelton,
and
K.M.Coombs
(2004).
Avian reovirus temperature-sensitive mutant tsA12 has a lesion in major core protein sigmaA and is defective in assembly.
|
| |
J Virol,
78,
11142-11151.
|
|
|
|
|
|
|
A.L.Odegard,
K.Chandran,
S.Liemann,
S.C.Harrison,
and
M.L.Nibert
(2003).
Disulfide bonding among micro 1 trimers in mammalian reovirus outer capsid: a late and reversible step in virion morphogenesis.
|
| |
J Virol,
77,
5389-5400.
|
|
|
|
|
|
|
A.Maraver,
A.Oña,
F.Abaitua,
D.González,
R.Clemente,
J.A.Ruiz-Díaz,
J.R.Castón,
F.Pazos,
and
J.F.Rodriguez
(2003).
The oligomerization domain of VP3, the scaffolding protein of infectious bursal disease virus, plays a critical role in capsid assembly.
|
| |
J Virol,
77,
6438-6449.
|
|
|
|
|
|
|
B.R.Bowman,
M.L.Baker,
F.J.Rixon,
W.Chiu,
and
F.A.Quiocho
(2003).
Structure of the herpesvirus major capsid protein.
|
| |
EMBO J,
22,
757-765.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.K.Limn,
and
P.Roy
(2003).
Intermolecular interactions in a two-layered viral capsid that requires a complex symmetry mismatch.
|
| |
J Virol,
77,
11114-11124.
|
|
|
|
|
|
|
I.Erk,
J.C.Huet,
M.Duarte,
S.Duquerroy,
F.Rey,
J.Cohen,
and
J.Lepault
(2003).
A zinc ion controls assembly and stability of the major capsid protein of rotavirus.
|
| |
J Virol,
77,
3595-3601.
|
|
|
|
|
|
|
K.Chandran,
J.S.Parker,
M.Ehrlich,
T.Kirchhausen,
and
M.L.Nibert
(2003).
The delta region of outer-capsid protein micro 1 undergoes conformational change and release from reovirus particles during cell entry.
|
| |
J Virol,
77,
13361-13375.
|
|
|
|
|
|
|
K.Chandran,
and
M.L.Nibert
(2003).
Animal cell invasion by a large nonenveloped virus: reovirus delivers the goods.
|
| |
Trends Microbiol,
11,
374-382.
|
|
|
|
|
|
|
M.J.Gage,
and
A.S.Robinson
(2003).
C-terminal hydrophobic interactions play a critical role in oligomeric assembly of the P22 tailspike trimer.
|
| |
Protein Sci,
12,
2732-2747.
|
|
|
|
|
|
|
M.von Grotthuss,
L.S.Wyrwicz,
and
L.Rychlewski
(2003).
mRNA cap-1 methyltransferase in the SARS genome.
|
| |
Cell,
113,
701-702.
|
|
|
|
|
|
|
T.Stehle,
and
T.S.Dermody
(2003).
Structural evidence for common functions and ancestry of the reovirus and adenovirus attachment proteins.
|
| |
Rev Med Virol,
13,
123-132.
|
|
|
|
|
|
|
W.Jiang,
Z.Li,
Z.Zhang,
M.L.Baker,
P.E.Prevelige,
and
W.Chiu
(2003).
Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions.
|
| |
Nat Struct Biol,
10,
131-135.
|
|
|
|
|
|
|
X.Wu,
and
L.A.Guarino
(2003).
Autographa californica nucleopolyhedrovirus orf69 encodes an RNA cap (nucleoside-2'-O)-methyltransferase.
|
| |
J Virol,
77,
3430-3440.
|
|
|
|
|
|
|
X.Zhang,
S.B.Walker,
P.R.Chipman,
M.L.Nibert,
and
T.S.Baker
(2003).
Reovirus polymerase lambda 3 localized by cryo-electron microscopy of virions at a resolution of 7.6 A.
|
| |
Nat Struct Biol,
10,
1011-1018.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Y.Miyanari,
M.Hijikata,
M.Yamaji,
M.Hosaka,
H.Takahashi,
and
K.Shimotohno
(2003).
Hepatitis C virus non-structural proteins in the probable membranous compartment function in viral genome replication.
|
| |
J Biol Chem,
278,
50301-50308.
|
|
|
|
|
|
|
A.Charpilienne,
J.Lepault,
F.Rey,
and
J.Cohen
(2002).
Identification of rotavirus VP6 residues located at the interface with VP2 that are essential for capsid assembly and transcriptase activity.
|
| |
J Virol,
76,
7822-7831.
|
|
|
|
|
|
|
B.Sherry
(2002).
The role of interferon regulatory factors in the cardiac response to viral infection.
|
| |
Viral Immunol,
15,
17-28.
|
|
|
|
|
|
|
D.H.Bamford
(2002).
Those magnificent molecular machines: logistics in dsRNA virus transcription.
|
| |
EMBO Rep,
3,
317-318.
|
|
|
|
|
|
|
G.Michel,
V.Sauvé,
R.Larocque,
Y.Li,
A.Matte,
and
M.Cygler
(2002).
The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot.
|
| |
Structure,
10,
1303-1315.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Naitow,
J.Tang,
M.Canady,
R.B.Wickner,
and
J.E.Johnson
(2002).
L-A virus at 3.4 A resolution reveals particle architecture and mRNA decapping mechanism.
|
| |
Nat Struct Biol,
9,
725-728.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.D.Chappell,
A.E.Prota,
T.S.Dermody,
and
T.Stehle
(2002).
Crystal structure of reovirus attachment protein sigma1 reveals evolutionary relationship to adenovirus fiber.
|
| |
EMBO J,
21,
1.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Kim,
X.Zhang,
V.E.Centonze,
V.D.Bowman,
S.Noble,
T.S.Baker,
and
M.L.Nibert
(2002).
The hydrophilic amino-terminal arm of reovirus core shell protein lambda1 is dispensable for particle assembly.
|
| |
J Virol,
76,
12211-12222.
|
|
|
|
|
|
|
K.Chandran,
D.L.Farsetta,
and
M.L.Nibert
(2002).
Strategy for nonenveloped virus entry: a hydrophobic conformer of the reovirus membrane penetration protein micro 1 mediates membrane disruption.
|
| |
J Virol,
76,
9920-9933.
|
|
|
|
|
|
|
M.I.Swanson,
Y.M.She,
W.Ens,
E.G.Brown,
and
K.M.Coombs
(2002).
Mammalian reovirus core protein micro 2 initiates at the first start codon and is acetylated.
|
| |
Rapid Commun Mass Spectrom,
16,
2317-2324.
|
|
|
|
|
|
|
M.J.Pirttimaa,
A.O.Paatero,
M.J.Frilander,
and
D.H.Bamford
(2002).
Nonspecific nucleoside triphosphatase P4 of double-stranded RNA bacteriophage phi6 is required for single-stranded RNA packaging and transcription.
|
| |
J Virol,
76,
10122-10127.
|
|
|
|
|
|
|
M.P.Egloff,
D.Benarroch,
B.Selisko,
J.L.Romette,
and
B.Canard
(2002).
An RNA cap (nucleoside-2'-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization.
|
| |
EMBO J,
21,
2757-2768.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Schwartz,
J.Chen,
M.Janda,
M.Sullivan,
J.den Boon,
and
P.Ahlquist
(2002).
A positive-strand RNA virus replication complex parallels form and function of retrovirus capsids.
|
| |
Mol Cell,
9,
505-514.
|
|
|
|
|
|
|
P.Ahlquist
(2002).
RNA-dependent RNA polymerases, viruses, and RNA silencing.
|
| |
Science,
296,
1270-1273.
|
|
|
|
|
|
|
S.D.Moore,
and
P.E.Prevelige
(2002).
DNA packaging: a new class of molecular motors.
|
| |
Curr Biol,
12,
R96-R98.
|
|
|
|
|
|
|
S.Liemann,
K.Chandran,
T.S.Baker,
M.L.Nibert,
and
S.C.Harrison
(2002).
Structure of the reovirus membrane-penetration protein, Mu1, in a complex with is protector protein, Sigma3.
|
| |
Cell,
108,
283-295.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.M.Olland,
J.Jané-Valbuena,
L.A.Schiff,
M.L.Nibert,
and
S.C.Harrison
(2001).
Structure of the reovirus outer capsid and dsRNA-binding protein sigma3 at 1.8 A resolution.
|
| |
EMBO J,
20,
979-989.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.Shao,
Z.H.Zhou,
and
G.Lu
(2001).
Three-dimensional structure of the inner core of rice dwarf virus.
|
| |
Sci China C Life Sci,
44,
192-198.
|
|
|
|
|
|
|
D.H.Bamford,
R.J.Gilbert,
J.M.Grimes,
and
D.I.Stuart
(2001).
Macromolecular assemblies: greater than their parts.
|
| |
Curr Opin Struct Biol,
11,
107-113.
|
|
|
|
|
|
|
E.Nogales,
and
N.Grigorieff
(2001).
Molecular Machines: putting the pieces together.
|
| |
J Cell Biol,
152,
F1-10.
|
|
|
|
|
|
|
J.B.Pesavento,
J.A.Lawton,
M.E.Estes,
and
B.V.Venkataram Prasad
(2001).
The reversible condensation and expansion of the rotavirus genome.
|
| |
Proc Natl Acad Sci U S A,
98,
1381-1386.
|
|
|
|
|
|
|
J.Lepault,
I.Petitpas,
I.Erk,
J.Navaza,
D.Bigot,
M.Dona,
P.Vachette,
J.Cohen,
and
F.A.Rey
(2001).
Structural polymorphism of the major capsid protein of rotavirus.
|
| |
EMBO J,
20,
1498-1507.
|
|
|
|
|
|
|
J.M.Bujnicki,
and
L.Rychlewski
(2001).
Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda 2 protein.
|
| |
Genome Biol,
2,
RESEARCH0038.
|
|
|
|
|
|
|
J.R.Castón,
J.L.Martínez-Torrecuadrada,
A.Maraver,
E.Lombardo,
J.F.Rodríguez,
J.I.Casal,
and
J.L.Carrascosa
(2001).
C terminus of infectious bursal disease virus major capsid protein VP2 is involved in definition of the T number for capsid assembly.
|
| |
J Virol,
75,
10815-10828.
|
|
|
|
|
|
|
M.M.Poranen,
A.O.Paatero,
R.Tuma,
and
D.H.Bamford
(2001).
Self-assembly of a viral molecular machine from purified protein and RNA constituents.
|
| |
Mol Cell,
7,
845-854.
|
|
|
|
|
|
|
M.Mathieu,
I.Petitpas,
J.Navaza,
J.Lepault,
E.Kohli,
P.Pothier,
B.V.Prasad,
J.Cohen,
and
F.A.Rey
(2001).
Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion.
|
| |
EMBO J,
20,
1485-1497.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.C.Harrison
(2001).
The familiar and the unexpected in structures of icosahedral viruses.
|
| |
Curr Opin Struct Biol,
11,
195-199.
|
|
|
|
|
|
|
Z.H.Zhou,
M.L.Baker,
W.Jiang,
M.Dougherty,
J.Jakana,
G.Dong,
G.Lu,
and
W.Chiu
(2001).
Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus.
|
| |
Nat Struct Biol,
8,
868-873.
|
|
|
|
|
|
|
D.H.Bamford
(2000).
Virus structures: Those magnificent molecular machines.
|
| |
Curr Biol,
10,
R558-R561.
|
|
|
|
|
|
|
E.L.Nason,
S.K.Samal,
and
B.V.Venkataram Prasad
(2000).
Trypsin-induced structural transformation in aquareovirus.
|
| |
J Virol,
74,
6546-6555.
|
|
|
|
|
|
|
E.V.Makeyev,
and
D.H.Bamford
(2000).
The polymerase subunit of a dsRNA virus plays a central role in the regulation of viral RNA metabolism.
|
| |
EMBO J,
19,
6275-6284.
|
|
|
|
|
|
|
G.G.Shipley
(2000).
Bilayers and nonbilayers: structure, forces and protein crystallization.
|
| |
Curr Opin Struct Biol,
10,
471-473.
|
|
|
|
|
|
|
T.Dokland
(2000).
Freedom and restraint: themes in virus capsid assembly.
|
| |
Structure,
8,
R157-R162.
|
|
|
|
|
|
|
Y.Tao,
and
W.Zhang
(2000).
Recent developments in cryo-electron microscopy reconstruction of single particles.
|
| |
Curr Opin Struct Biol,
10,
616-622.
|
|
|
|
|
|
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
