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Figure 1.
FIGURE 1. A, stereo view of the ribbon diagram of Atg3. The
 -helices are lettered
and indicated with red helical ribbons, and  -strands are numbered
and indicated with cyan arrows. Residues adjacent to the
disordered regions are numbered. B, structural comparison of
Atg3 with Ubc9. Ribbon diagrams (top) and topologies (bottom) of
Atg3 and Ubc9 (Protein Data Bank code 1U9A) are shown in the
same orientation. Conserved -helices and -strands
are colored red and cyan, respectively, and nonconserved -helices, -strands,
and loop regions are colored gray. The two unique inserted
regions of Atg3, FR and HR, are colored yellow. Numbering and
labeling of secondary structural elements are based on Atg3.
Amino and carboxyl termini are denoted N and C, respectively,
and the catalytic cysteine of Atg3 and Ubc9 is indicated with a
stick model (top) and a circled letter (bottom). C, ribbon
diagram of the catalytic site of Atg3 (left) and Ubc9 (right).
The side chains of Cys-234 (Atg3) and Cys-93 (Ubc9) as well as
their surrounding residues are shown with stick models and are
colored yellow, red, and blue for sulfur, oxygen, and nitrogen
atoms, respectively. A sulfate ion observed in the Atg3
structure is also shown with a stick model. Hydrogen bonds
between Pro-233 and Val-239 of Atg3 and between Cys-93 and
Asn-85 of Ubc9 are shown with broken lines. The figure was
prepared using PyMOL (35).
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