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Figure 6.
Figure 6. Structure of Two-Domain N-Cadherin and Comparison
of Strand Dimer Surfaces(A) Stereo view of a representative
region from the electron density map calculated with 2|F[o] −
F[c]| coefficients contoured at 1.0 σ (blue). A portion of the
Bijvoet difference Fourier map for the selenomethionyl protein,
contoured at 5.0 σ, is shown in cyan. The position of the peak
in this map corresponds to the position of the selenium atom
from selenomethionine 128.(B) α-carbon trace of the refined
N-cadherin D1D2 protomer superimposed on the Bijvoet difference
Fourier map contoured at 5.0 σ. The position of the selenium
atom from every selenomethionine residue in the protein is
clearly seen in the difference map, and these positions match
the refined model. “U” marks the site of a uranyl ion, which
also has anomalous diffraction properties at the selenium edge
energy. Figure prepared with the program TOM ([11]).(C)
Ca^2+-binding site of N-cadherin D1D2. Each amino acid that
donates ligands from its side chain is labeled; Bonds to oxygen
atoms are shown in red, nitrogen atoms are shown in blue, and
Ca^2+ ions are drawn as green spheres. Figure prepared with
SETOR ([6]).(D) Crystal interface [(x,1 − y,1 − z) symmetry
mate in space group I422] that shows an antiparallel interaction
at the adhesive face of the D1 domain of N-cadherin. This
interface has similarities to, yet is distinct from, the
putative adhesive interface suggested previously ([26]). Inset
shows a close-up view of this interface. Interactions between
side chains are almost exclusively hydrophobic. Figure prepared
with GRASP ( [17]).(E) Superposition of N-cadherin (white) with
E-cadherin (orange). The D2 domains have been superposed,
illustrating the relative motions between domains as
displacemant of the D1 domain.(F) Molecular surface of one
monomer of N-cadherin with the part of the A strand from its
strand dimer partner drawn as a stick model (from Protein Data
Bank accession 1NCG). Note the complete intercalation of the
Trp-2 side chain.(G) Molecular surfaces of N- and E-cadherin
crystal structures. Convex surface features are drawn in green,
and concave features are drawn in gray. The arrows point to the
Trp-2 acceptor pocket, which is a conserved structural feature
of the one-domain N-cadherin structures ([26]), two-domain
N-cadherin structure (this work), and two-domain E-cadherin
structure ( [16]). Figure prepared with GRASP ( [17]).
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