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Figure 1.
Figure 1. Three-Dimensional Solution Structure of the
AIRE-PHD1/H3K4me0 Peptide Complex
(A) Schematic
representation of the functional domains in the human AIRE
protein. Grey boxes represent HSR (homogenously staining
region), PHD (plant homeodomain), and SAND (Sp100, AIRE-1,
NucP41/P75, and Drosophila DEAF-1). PHD and SAND domain
boundaries are based on Pfam HMM (Bateman et al., 1999) and
remaining segments are based on Meloni et al. (2008). AIRE-PHD1
studied here is shown in blue.
(B) Backbone atoms (N, Cα,
and C′) of the 20 superposed NMR structures of the AIRE-PHD1
where protein and peptide are gray and yellow, respectively
(left).
(C) Ribbon representation of the complex (middle)
highlights the secondary structural elements (protein, blue;
peptide, yellow). Pink spheres represent Zn atoms. Only a single
representation of Zn atoms of the lowest energy structure is
shown in the ensemble for clarity.
(D) Electrostatic
potential (isocontour value of ±70 kT/e) surface
representation of the AIRE-PHD1 bound to the H3K4me0 peptide
(yellow).
(E) Backbone protein-peptide interactions with
inset showing the H3A1 interacting neighborhood. The peptide and
protein residues are color coded by atom type with carbon atoms
in yellow and green, respectively. The orientation of the
peptide is the same as that in (C).
(F) Key protein-peptide
side-chain interactions with insets respectively highlighting
R2, K4, and T3 neighborhood and their surface grooves. The
nonpolar nonbonded interacting atoms are labeled with ↔. The
peptide orientation in the stick representation is depicted as
in the ribbon diagram on left.
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