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Figure 1.
Figure 1. Stereo views of FabE8-cyt c complex and FabE8
X-ray structures. a, Ribbon representation of the FabE8-cyt c
interface region. E8 V-domain (V[L], white; V[H], yellow) and
cyt c (orange). Highlighted are the three major discontiguous
segments of E8 epitope on cyt c (33 to 39, 56 to 66 and 96 to
104 in red) and the six E8 CDRs (L1 and H1, red; L2 and H2,
yellow; L3 and H3, green). b, Ribbon representation of the FabE8
(pink) and FabE8-cyt c (L, white; H, yellow; cyt c, orange)
structures with V-domains superimposed. The elbow angles of the
two structures differ by 6°. c, Cyt c (orange) bound to
CDR-H3 of FabE8-cyt c (yellow), with CDR-H3 of D1.3Fv-HEL
(purple) superimposed. The tip of E8 H3 (top) complements the
second 30 s type II b-turn (35 to 38) of cyt c. E8 Phe91L and
Trp96L of L3 (white) and Tyr33H1 (yellow) neighbour E8 H3. The
base of E8 H3 is in the extended conformation and the
carboxylate group of Asp105H3[101] hydrogen bonds with the
Trp107H[103] FR4 and Tyr36L FR2 side-chains. In the D1.3
antibody (purple), the base of H3 is "kinked" at position [101].
The Asp side-chain at this position is flipped 180° with
respect to E8 Asp105H3[101] and ion pairs with ArgH3[94]
(equivalent position Gly98H in E8). Oxygen and nitrogen atoms
are shown as red and blue spheres, respectively and hydrogen
bonds as yellow dotted lines.
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