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composed of 30 segments of RNA duplex closely associated with the
capsid. In the reconstruction of MGNNV, there is no significant
density adjacent to the capsid that can be interpreted as duplex RNA.
However, the density at lower radius (112 Å) may be attributed to
the cellular RNA randomly packaged inside the capsid and/or por-
tions of the coat protein, e.g. the N-terminal basic-residue-rich seg-
ments that are likely to interact with RNA.
Modeling the Domain Structure of MGNNV
Capsid Protein
The MGNNV capsid protein shows no significant sequence homol-
ogy with any known insect nodavirus. We used 3D-PSSM (three-
dimensional position-specific scoring matrix) to investigate the folding
motif of the MGNNV coat protein.
5
Four structures were identified
as comparable with MGNNV with a confidence level of 95%, while
the rest of the candidates had a confidence level of 50%. Strikingly,
there were no insect nodaviruses with known atomic structure in the
top 20 comparable structures. All four structures identified as likely
homologues of MGNNV were virus coat proteins that have canon-
ical, uninterrupted viral
-sandwich folds. The first three varied from
189 to 222 aligned residues, and they predicted the fold of MGNNV
residues 31 to 235, 49 to 214, and 27 to 213, respectively, as a
β
β
-sandwich (Fig. 2). The fourth structure provided prediction for
almost the entire MGNNV sequence (residues 24 to 319). The fourth
structure was the coat protein of tomato bushy stunt virus (TBSV),
which contains two domains: the N-terminal domain (residues 103 to
271) forming a
-sandwich and the contiguous protein capsid, and
the C-terminal domain (residues 272 to 387) forming a protrusion at
the capsid surface. Sequence comparisons of the coat proteins of
several fish nodaviruses showed that the protein could be divided into
a conserved region and a variable region. The conserved region com-
prises residues 83 to 216 and shows pairwise sequence identity of 86%
to 96%; the variable region comprises residues 235 to 315, with pair-
wise sequence identity of 66% to 84%. These results suggest that
residues 83 to 216 of MGNNV might form a conserved
β
β
-sandwich
