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Figure 2.
Top and middle, the C  atom
traces of the four proteins (15 crystallographically independent
structures) are superimposed: wild-type ubiquitin (three
molecules from orthorhombic P2[1]2[1]2[1] space group^*, gray);
[D-Gln35]ubiquitin (three molecules from P2[1]2[1]2[1]^*, red,
and two molecules from cubic P4[3]32 space group, pink);
[D-Val35]ubiquitin (two molecules from P4[3]32, green); and
[L-Gln35]ubiquitin (two molecules from P4[3]32, yellow). All C
atoms
were used in the superposition. Residue 35 is marked with a
black arrow. Side views are shown in the top panels and top
views in the middle panels. Bottom, superposition of ten
residues (residue 30–39) near residue 35. The main-chain atoms
of the four X-ray structures are shown: wild-type ubiquitin
(P2[1]2[1]2[1]^*, gray); [D-Gln35]ubiquitin (P4[3]32, pink);
[D-Val35]ubiquitin (P4[3]32, green); and [L-Gln35]ubiquitin
(P4[3]32, yellow). The main-chain conformation of residues
30–39 is very similar in all four structures (r.m.s.
deviations <0.2 Å), and only one molecule from each
crystal form is shown for clarity. ^* denotes ubiquitin
molecules taken from our previously reported structures in
P2[1]2[1]2[1] space group: orthorhombic wild-type ubiquitin (PDB
accession code 1YIW) and orthorhombic [D-Gln35]ubiquitin (1YJ1),
both of whose structures have been deposited previously^13. The
PDB codes for the cubic P4[3]32 structures of the four synthetic
ubiquitins are listed in the Methods.
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