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PDBsum entry 2bfv
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Immunoglobulin
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PDB id
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2bfv
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Antibody fragment fv4155 bound to two closely related steroid hormones: the structural basis of fine specificity.
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Authors
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C.H.Trinh,
S.D.Hemmington,
M.E.Verhoeyen,
S.E.Phillips.
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Ref.
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Structure, 1997,
5,
937-948.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: The concentration of steroid glucuronides in serial samples of early
morning urine (EMU) can be used to predict the fertile period in the female
menstrual cycle. The monoclonal antibody 4155 has been used as a convenient
means of measuring the concentration of steroid glucuronides in EMU, as it
specifically recognises the steroid hormone estrone beta-D-glucuronide (E3G),
with very high affinity, and the closely related hormone estriol
3-(beta-d-glucuronide) (EI3G), with reduced affinity. Although 4115 binds these
hormones with different affinities, EI3G differs from E3G only in the addition
of a hydroxyl group and reduction of an adjacent carbonyl. To investigate the
structural basis of this fine binding specificity, we have determined the
crystal structures of the variable fragment (Fv) of 4155 in complex with each of
these hormones. RESULTS: Two crystal forms of the Fv4155-EI3G complex, at
resolutions of 2.1 A and 2.5 A, and one form of the Fv4155-E3G complex, at 2.1 A
resolution were solved and refined. The crystal structures show the E3G or EI3G
antigen lying in an extended cleft, running form the centre of the antibody
combining site down one side of the variable domain interface, and formed almost
entirely from residues in the heavy chain. The binding cleft lies primarily
between the heavy chain complementarity determining regions (CDRs), rather than
in the interface between the heavy and light chains. In both complexes the
binding of the glucuronic sugar, and rings A and B of the steroid, is specified
by the shape of the narrow cleft. Analysis of the Fv structure reveals that five
of the six CDR regions can be assigned to one of the predefined canonical
structural classes. CONCLUSIONS: The difference in the binding affinity of
Fv4155 for the two steroid hormones is accounted for by a subtle combination of
a less favoured hydrogen-bond geometry, and a minor rearrangement of the water
molecule network around the binding site. The rearrangement of water molecules
results from the burial of the additional hydroxyl group of the EI3G in a
hydrophobic environment.
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Figure 2.
Figure 2. The overall fold of the Fv fragment, Fv4155. (a)
Stereoview of the Ca tracing of Fv4155. The N and C termini and
every tenth residue are labelled for both the light (L; purple)
and heavy (H; green) chains; Ca positions are marked by black
spheres. (b) A ribbon diagram of the Fv fragment Fv4155 in the
same orientation as (a). The V[L] and V[H] chains are coloured
purple and green, respectively. The bound E3G molecule is shown
in white ball-and-stick representation. (Figures were generated
using the programs MOLSCRIPT [51] and Raster 3D [52].)
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1997,
5,
937-948)
copyright 1997.
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