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PDBsum entry 1nmc
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Complex (single-chain antibody/antigen)
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PDB id
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1nmc
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Contents |
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388 a.a.
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122 a.a.
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109 a.a.
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Three-Dimensional structures of single-Chain fv-Neuraminidase complexes.
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Authors
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R.L.Malby,
A.J.Mccoy,
A.A.Kortt,
P.J.Hudson,
P.M.Colman.
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Ref.
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J Mol Biol, 1998,
279,
901-910.
[DOI no: ]
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PubMed id
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Abstract
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The structure of the complex between a recombinant single-chain Fv construct of
antibody NC10 with a five-residue peptide linker between VH and VL (termed
scFv(5)), and its antigen, tetrameric neuraminidase from influenza virus (NA),
has been determined and refined at 2.5 A resolution. The antibody-antigen
binding interface is very similar to that of a similar NC10 scFv-NA complex in
which the scFv has a 15-residue peptide linker (scFv(15)), and the NC10 Fab-NA
complex. However, scFv(5) and scFv(15) have different stoichiometries in
solution. While scFv(15) is predominantly monomeric in solution, scFv(5) forms
dimers exclusively, because the five-residue linker is not long enough to permit
VH and VL domains from the same polypeptide associating and forming an
antigen-binding site. Upon forming a complex with NA, scFv(15) forms a
approximately 300 kDa complex corresponding to one NA tetramer binding four
scFv(15) monomers, while scFv(5) forms a approximately 590 kDa complex,
corresponding to two NA tetramers crosslinked by four bivalent scFv(5) dimers.
However, the dimeric scFv(5) in the scFv(5)-NA crystals does not crosslink NA
tetramers, and modelling studies indicate that it is not possible to pack four
dimeric and simultaneously bivalent scFvs between the NA tetramers with only a
five-residue linker between VH and VL. The inability arises from the exacting
requirement to orient the two antigen-binding surfaces to bind the tetrameric NA
antigen while avoiding steric clashes with NC10 scFv(5) dimers bound to other
sites on the NA tetramer. The utility of bivalent or bifunctional scFvs with
short linkers may therefore be restricted by the steric constraints imposed by
binding multivalent antigens.
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Figure 1.
Figure 1. Model of the  vert,
similar 590 kDa complex observed in solution studies of the NC10
scFv(5)-NA, in which the scFv(5) is dimeric and bivalent [Kortt
et al 1997]. Model is shown as a bold C^αtrace. The NA
tetramers (green and purple) are crosslinked by scFv(5)
molecules. The Fv domain bound to the green NA is shown with
V[L]yellow and V[H]orange, while the Fv domain bound to the
purple NA is shown with V[L]light blue and V[H]dark blue. The
scFv(5) is thus shown with one V[L]yellow and the other light
blue, and one V[H]orange and the other dark-blue. The complex
has point group 422 symmetry. Drawn with MOLSCRIPT [Kraulis
1991] and RASTER3D [Bacon and Anderson 1989 and Merritt and
Murphy 1994]. (a) View with the molecular 4-fold axis vertical.
(b) View with the molecular 4-fold axis out of the page.
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Figure 3.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
279,
901-910)
copyright 1998.
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Secondary reference #1
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Title
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Recombinant antineuraminidase single chain antibody: expression, Characterization, And crystallization in complex with antigen.
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Authors
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R.L.Malby,
J.B.Caldwell,
L.C.Gruen,
V.R.Harley,
N.Ivancic,
A.A.Kortt,
G.G.Lilley,
B.E.Power,
R.G.Webster,
P.M.Colman.
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Ref.
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Proteins, 1993,
16,
57-63.
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PubMed id
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