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* Residue conservation analysis
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J Virol
72:4610-4622
(1998)
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PubMed id:
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Antibody-mediated neutralization of human rhinovirus 14 explored by means of cryoelectron microscopy and X-ray crystallography of virus-Fab complexes.
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Z.Che,
N.H.Olson,
D.Leippe,
W.M.Lee,
A.G.Mosser,
R.R.Rueckert,
T.S.Baker,
T.J.Smith.
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ABSTRACT
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The structures of three different human rhinovirus 14 (HRV14)-Fab complexes have
been explored with X-ray crystallography and cryoelectron microscopy procedures.
All three antibodies bind to the NIm-IA site of HRV14, which is the
beta-B-beta-C loop of the viral capsid protein VP1. Two antibodies, Fab17-IA
(Fab17) and Fab12-IA (Fab12), bind bivalently to the virion surface and strongly
neutralize viral infectivity whereas Fab1-IA (Fab1) strongly aggregates and
weakly neutralizes virions. The structures of the two classes of virion-Fab
complexes clearly differ and correlate with observed binding neutralization
differences. Fab17 and Fab12 bind in essentially identical, tangential
orientations to the viral surface, which favors bidentate binding over
icosahedral twofold axes. Fab1 binds in a more radial orientation that makes
bidentate binding unlikely. Although the binding orientations of these two
antibody groups differ, nearly identical charge interactions occur at all
paratope-epitope interfaces. Nucleotide sequence comparisons suggest that Fab17
and Fab12 are from the same progenitor cell and that some of the differing
residues contact the south wall of the receptor binding canyon that encircles
each of the icosahedral fivefold vertices. All of the antibodies contact a
significant proportion of the canyon region and directly overlap much of the
receptor (intercellular adhesion molecule 1 [ICAM-1]) binding site. Fab1,
however, does not contact the same residues on the upper south wall (the side
facing away from fivefold axes) at the receptor binding region as do Fab12 and
Fab17. All three antibodies cause some stabilization of HRV14 against pH-induced
inactivation; thus, stabilization may be mediated by invariant contacts with the
canyon.
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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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S.Taube,
J.R.Rubin,
U.Katpally,
T.J.Smith,
A.Kendall,
J.A.Stuckey,
and
C.E.Wobus
(2010).
High-resolution x-ray structure and functional analysis of the murine norovirus 1 capsid protein protruding domain.
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J Virol,
84,
5695-5705.
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PDB codes:
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S.Hafenstein,
V.D.Bowman,
T.Sun,
C.D.Nelson,
L.M.Palermo,
P.R.Chipman,
A.J.Battisti,
C.R.Parrish,
and
M.G.Rossmann
(2009).
Structural comparison of different antibodies interacting with parvovirus capsids.
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J Virol,
83,
5556-5566.
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PDB codes:
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T.Kiyohara,
A.Totsuka,
T.Yoneyama,
K.Ishii,
T.Ito,
and
T.Wakita
(2009).
Characterization of anti-idiotypic antibodies mimicking antibody- and receptor-binding sites on hepatitis A virus.
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Arch Virol,
154,
1263-1269.
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U.Katpally,
T.M.Fu,
D.C.Freed,
D.R.Casimiro,
and
T.J.Smith
(2009).
Antibodies to the buried N terminus of rhinovirus VP4 exhibit cross-serotypic neutralization.
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J Virol,
83,
7040-7048.
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U.Katpally,
C.E.Wobus,
K.Dryden,
H.W.Virgin,
and
T.J.Smith
(2008).
Structure of antibody-neutralized murine norovirus and unexpected differences from viruslike particles.
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J Virol,
82,
2079-2088.
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C.D.Nelson,
L.M.Palermo,
S.L.Hafenstein,
and
C.R.Parrish
(2007).
Different mechanisms of antibody-mediated neutralization of parvoviruses revealed using the Fab fragments of monoclonal antibodies.
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Virology,
361,
283-293.
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P.M.Day,
C.D.Thompson,
C.B.Buck,
Y.Y.Pang,
D.R.Lowy,
and
J.T.Schiller
(2007).
Neutralization of human papillomavirus with monoclonal antibodies reveals different mechanisms of inhibition.
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J Virol,
81,
8784-8792.
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J.D.Uram,
K.Ke,
A.J.Hunt,
and
M.Mayer
(2006).
Submicrometer pore-based characterization and quantification of antibody-virus interactions.
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Small,
2,
967-972.
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S.K.Lal,
P.Kumar,
W.M.Yeo,
A.Kar-Roy,
and
V.T.Chow
(2006).
The VP1 protein of human enterovirus 71 self-associates via an interaction domain spanning amino acids 66-297.
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J Med Virol,
78,
582-590.
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L.Govindasamy,
K.Hueffer,
C.R.Parrish,
and
M.Agbandje-McKenna
(2003).
Structures of host range-controlling regions of the capsids of canine and feline parvoviruses and mutants.
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J Virol,
77,
12211-12221.
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PDB codes:
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S.A.Hardy,
and
N.J.Dimmock
(2003).
Valency of antibody binding to enveloped virus particles as determined by surface plasmon resonance.
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J Virol,
77,
1649-1652.
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J.E.Ludert,
M.C.Ruiz,
C.Hidalgo,
and
F.Liprandi
(2002).
Antibodies to rotavirus outer capsid glycoprotein VP7 neutralize infectivity by inhibiting virion decapsidation.
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J Virol,
76,
6643-6651.
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J.Navaza,
J.Lepault,
F.A.Rey,
C.Alvarez-Rúa,
and
J.Borge
(2002).
On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation.
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Acta Crystallogr D Biol Crystallogr,
58,
1820-1825.
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M.G.Rossmann,
Y.He,
and
R.J.Kuhn
(2002).
Picornavirus-receptor interactions.
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Trends Microbiol,
10,
324-331.
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V.D.Bowman,
E.S.Chase,
A.W.Franz,
P.R.Chipman,
X.Zhang,
K.L.Perry,
T.S.Baker,
and
T.J.Smith
(2002).
An antibody to the putative aphid recognition site on cucumber mosaic virus recognizes pentons but not hexons.
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J Virol,
76,
12250-12258.
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M.E.Bloom,
S.M.Best,
S.F.Hayes,
R.D.Wells,
J.B.Wolfinbarger,
R.McKenna,
and
M.Agbandje-McKenna
(2001).
Identification of aleutian mink disease parvovirus capsid sequences mediating antibody-dependent enhancement of infection, virus neutralization, and immune complex formation.
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J Virol,
75,
11116-11127.
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A.M.Roseman
(2000).
Docking structures of domains into maps from cryo-electron microscopy using local correlation.
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Acta Crystallogr D Biol Crystallogr,
56,
1332-1340.
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E.Thouvenin,
and
E.Hewat
(2000).
When two into one won't go: fitting in the presence of steric hindrance and partial occupancy.
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Acta Crystallogr D Biol Crystallogr,
56,
1350-1357.
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S.Monaco-Malbet,
C.Berthet-Colominas,
A.Novelli,
N.Battaï,
N.Piga,
V.Cheynet,
F.Mallet,
and
S.Cusack
(2000).
Mutual conformational adaptations in antigen and antibody upon complex formation between an Fab and HIV-1 capsid protein p24.
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Structure,
8,
1069-1077.
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PDB codes:
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Y.Tao,
and
W.Zhang
(2000).
Recent developments in cryo-electron microscopy reconstruction of single particles.
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Curr Opin Struct Biol,
10,
616-622.
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J.A.Lawton,
M.K.Estes,
and
B.V.Prasad
(1999).
Comparative structural analysis of transcriptionally competent and incompetent rotavirus-antibody complexes.
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Proc Natl Acad Sci U S A,
96,
5428-5433.
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P.R.Kolatkar,
J.Bella,
N.H.Olson,
C.M.Bator,
T.S.Baker,
and
M.G.Rossmann
(1999).
Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor.
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EMBO J,
18,
6249-6259.
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PDB codes:
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T.S.Baker,
N.H.Olson,
and
S.D.Fuller
(1999).
Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs.
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Microbiol Mol Biol Rev,
63,
862.
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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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Links
