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The crystal structure of the complex between neuraminidase from influenza virus
(subtype N9 and isolated from an avian source) and the antigen-binding fragment
(Fab) of monoclonal antibody NC41 has been refined by both least-squares and
simulated annealing methods to an R-factor of 0.191 using 31,846 diffraction
data in the resolution range 8.0 to 2.5 A. The resulting model has a
root-mean-square deviation from ideal bond-length of 0.016 A. One fourth of the
tetrameric complex comprises the crystallographic model, which has 6577
non-hydrogen atoms and consists of 389 protein residues and eight carbohydrate
residues in the neuraminidase, 214 residues in the Fab light chain, and 221
residues in the heavy chain. One putative Ca ion buried in the neuraminidase,
and 73 water molecules, are also included. A remarkable shape complementarity
exists between the interacting surfaces of the antigen and the antibody,
although the packing density of atoms at the interface is somewhat looser than
in the interior of a protein. Similarly, there is a high degree of chemical
complementarity between the antigen and antibody, mediated by one buried
salt-link, two solvated salt-links and 12 hydrogen bonds. The antibody-binding
site on neuraminidase is discontinuous and comprises five chain segments and 19
residues in contact, whilst 33 neuraminidase residues in eight segments have 899
A2 of surface area buried by the interaction (to a 1.7 A probe), including two
hexose units. Seventeen residues in NC41 Fab lying in five of the six
complementarity determining regions (CDRs) make contact with the neuraminidase
and 36 antibody residues in seven segments have 916 A2 of buried surface area.
The interface is more extensive than those of the three lysozyme-Fab complexes
whose crystal structures have been determined, as judged by buried surface area
and numbers of contact residues. There are only small differences (less than 1.5
A) between the complexed and uncomplexed neuraminidase structures and, at this
resolution and accuracy, those differences are not unequivocal. The main-chain
conformations of five of the CDRs follow the predicted canonical structures. The
interface between the variable domains of the light and heavy chains is not as
extensive as in other Fabs, due to less CDR-CDR interaction in NC41. The first
CDR on the NC41 Fab light chain is positioned so that it could sterically hinder
the approach of small as well as large substrates to the neuraminidase
active-site pocket, suggesting a possible mechanism for the observed inhibition
of enzyme activity by the antibody.(ABSTRACT TRUNCATED AT 400 WORDS)
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