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Figure 2.
Fig. 2. Three-dimensional structures of HA1–sugar complex
and F[o] − F[c] omit maps for the ligands with 2.0 σ
contoured level. (a) The overall structure of the HA1–Neu5Ac
complex. There are two molecules (Mol-A and Mol-B) in an
asymmetric unit; Mol-A and Mol-B are structurally almost
identical. HA1 is composed of two β-trefoil domains, N- and
C-terminal domains, linked by an α-helix (gray). The three
repeats of each domain are displayed in lime green (α-repeat),
blue (β-repeat), and magenta (γ-repeat). Two Neu5Ac molecules
are indicated by the stick models. The ligands are found at
binding sites I and III. At the site I position, Neu5Ac
molecules are found not only in Mol-A but also in Mol-B (site
I[B]). The binding sites I[A] and I[B] illustrated in the
figures are in the equivalent position for each molecule. At the
position indicated as binding site III, Neu5Ac is only seen in
Mol-A. (b) The HA1–Gal complex structure. Gal molecules are
seen at site I[B] located at the 2α-repeat and at site II
located at the 2γ-repeat of Mol-B; no electron density for the
ligands was observed for Mol-A. The β-strands of 2α- and
2γ-repeat (site I and II) were numbered. (c) The density of
Neu5Ac located at binding sites I and III. At binding site I[B],
the electron density of the sugar is clearly seen, almost to the
same degree as that at binding site I (data not shown). The
electron density of Neu5Ac observed at site II is relatively
weak. (d) The electron density of GalNAc located at binding site
I[B]. (e) The density of Gal located at binding sites I[B] and
II[B].
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