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PDBsum entry 2o5z
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Immune system
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PDB id
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2o5z
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References listed in PDB file
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Key reference
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Title
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Closely related antibody receptors exploit fundamentally different strategies for steroid recognition.
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Authors
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P.Verdino,
C.Aldag,
D.Hilvert,
I.A.Wilson.
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Ref.
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Proc Natl Acad Sci U S A, 2008,
105,
11725-11730.
[DOI no: ]
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PubMed id
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Abstract
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Molecular recognition by the adaptive immune system relies on specific
high-affinity antibody receptors that are generated from a restricted set of
starting sequences through homologous recombination and somatic mutation. The
steroid binding antibody DB3 and the catalytic Diels-Alderase antibody 1E9
derive from the same germ line sequences but exhibit very distinct specificities
and functions. However, mutation of only two of the 36 sequence differences in
the variable domains, Leu(H47)Trp and Arg(H100)Trp, converts 1E9 into a
high-affinity steroid receptor with a ligand recognition profile similar to DB3.
To understand how these changes switch binding specificity and function, we
determined the crystal structures of the 1E9 Leu(H47)Trp/Arg(H100)Trp double
mutant (1E9dm) as an unliganded Fab at 2.05 A resolution and in complex with two
configurationally distinct steroids at 2.40 and 2.85 A. Surprisingly, despite
the functional mimicry of DB3, 1E9dm employs a distinct steroid binding
mechanism. Extensive structural rearrangements occur in the combining site,
where residue H47 acts as a specificity switch and H100 adapts to different
ligands. Unlike DB3, 1E9dm does not use alternative binding pockets or different
sets of hydrogen-bonding interactions to bind configurationally distinct
steroids. Rather, the different steroids are inserted more deeply into the 1E9dm
combining site, creating more hydrophobic contacts that energetically compensate
for the lack of hydrogen bonds. These findings demonstrate how subtle mutations
within an existing molecular scaffold can dramatically modulate the function of
immune receptors by inducing unanticipated, but compensating, mechanisms of
ligand interaction.
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Figure 3.
Ligand binding by Diels–Alderase 1E9 (A), 1E9dm (B), and
the steroid-binding DB3 (C). (Left) Proteins are shown in the
same orientation to demonstrate the distinct shapes of the
combining sites and the different ways in which the respective
ligands are bound. Light yellow, 1E9 TSA; cyan, progesterone;
orange, 5β-androstane-3,17-dione and two ordered water
molecules. (Right) 2D schemes of the ligand binding modes are
shown. Green, polar residues; brown, hydrophobic; blue-lined
circle, basic; red-lined circle, acidic; gray dashed line,
proximity contour; fuzzy blue, ligand exposure; blue underlayed
circle, receptor exposure; green arrow, side chain donor; olive
line, solvent contact.
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Figure 4.
Overlay of the combining sites of 1E9, 1E9dm, and DB3 with
bound ligands. (A) 1E9 and its TSA (gray) superimposed with
1E9dm binding progesterone (cyan). This view is rotated around
the z axis ≈90° compared with B–D to demonstrate the
movement of the Trp^H50 side chain in 1E9dm caused by the
Leu^H47Trp mutation. (B) The TSA bound by 1E9 (gray) and
5β-androstane-3,17-dione bound by 1E9dm (orange). (C)
Progesterone bound by 1E9dm in the inverse head-to-tail binding
mode with a buried A ring (cyan). The same steroid bound by DB3
(gray). (D) 5β-androstane-3,17-dione bound by 1E9dm (orange)
and DB3 (gray).
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