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* Residue conservation analysis
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DOI no:
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Structure
5:937-948
(1997)
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PubMed id:
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Antibody fragment Fv4155 bound to two closely related steroid hormones: the structural basis of fine specificity.
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C.H.Trinh,
S.D.Hemmington,
M.E.Verhoeyen,
S.E.Phillips.
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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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Selected figure(s)
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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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Figure was
selected
by the author.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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M.H.Niemi,
K.Takkinen,
L.K.Amundsen,
H.Söderlund,
J.Rouvinen,
and
M.Höyhtyä
(2011).
The testosterone binding mechanism of an antibody derived from a naïve human scFv library.
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J Mol Recognit,
24,
209-219.
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PDB code:
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M.Ui,
Y.Tanaka,
T.Tsumuraya,
I.Fujii,
M.Inoue,
M.Hirama,
and
K.Tsumoto
(2011).
Structural and energetic hot-spots for the interaction between a ladder-like polycyclic ether and the anti-ciguatoxin antibody 10C9Fab.
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Mol Biosyst,
7,
793-798.
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P.Scheerer,
A.Kramer,
L.Otte,
M.Seifert,
H.Wessner,
C.Scholz,
N.Krauss,
J.Schneider-Mergener,
and
W.Höhne
(2007).
Structure of an anti-cholera toxin antibody Fab in complex with an epitope-derived D-peptide: a case of polyspecific recognition.
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J Mol Recognit,
20,
263-274.
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PDB code:
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P.J.Kundrotas,
and
E.Alexov
(2006).
Electrostatic properties of protein-protein complexes.
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Biophys J,
91,
1724-1736.
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A.Yokota,
K.Tsumoto,
M.Shiroishi,
H.Kondo,
and
I.Kumagai
(2003).
The role of hydrogen bonding via interfacial water molecules in antigen-antibody complexation. The HyHEL-10-HEL interaction.
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J Biol Chem,
278,
5410-5418.
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PDB codes:
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I.Kumagai,
Y.Nishimiya,
H.Kondo,
and
K.Tsumoto
(2003).
Structural consequences of target epitope-directed functional alteration of an antibody. The case of anti-hen lysozyme antibody, HyHEL-10.
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J Biol Chem,
278,
24929-24936.
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PDB codes:
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L.C.James,
and
D.S.Tawfik
(2003).
The specificity of cross-reactivity: promiscuous antibody binding involves specific hydrogen bonds rather than nonspecific hydrophobic stickiness.
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Protein Sci,
12,
2183-2193.
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L.C.James,
P.Roversi,
and
D.S.Tawfik
(2003).
Antibody multispecificity mediated by conformational diversity.
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Science,
299,
1362-1367.
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PDB codes:
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J.Valjakka,
A.Hemminki,
S.Niemi,
H.Söderlund,
K.Takkinen,
and
J.Rouvinen
(2002).
Crystal structure of an in vitro affinity- and specificity-matured anti-testosterone Fab in complex with testosterone. Improved affinity results from small structural changes within the variable domains.
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J Biol Chem,
277,
44021-44027.
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PDB codes:
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J.Valjakka,
K.Takkinenz,
T.Teerinen,
H.Söderlund,
and
J.Rouvinen
(2002).
Structural insights into steroid hormone binding: the crystal structure of a recombinant anti-testosterone Fab fragment in free and testosterone-bound forms.
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J Biol Chem,
277,
4183-4190.
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PDB codes:
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S.Coulon,
J.L.Pellequer,
T.Blachère,
M.Chartier,
E.Mappus,
S.W.Chen Sw,
C.Y.Cuilleron,
and
D.Baty
(2002).
Functional characterization of an anti-estradiol antibody by site-directed mutagenesis and molecular modelling: modulation of binding properties and prominent role of the V(L) domain in estradiol recognition.
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J Mol Recognit,
15,
6.
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F.Bettsworth,
C.Monnet,
B.Watelet,
N.Battail-Poirot,
B.Gilquin,
M.Jolivet,
A.Menez,
M.Arnaud,
and
F.Ducancel
(2001).
Functional characterization of two anti-estradiol antibodies as deduced from modelling and site-directed mutagenesis experiments.
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J Mol Recognit,
14,
99.
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S.Spinelli,
L.G.Frenken,
P.Hermans,
T.Verrips,
K.Brown,
M.Tegoni,
and
C.Cambillau
(2000).
Camelid heavy-chain variable domains provide efficient combining sites to haptens.
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Biochemistry,
39,
1217-1222.
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PDB code:
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U.Lamminmäki,
and
J.Kankare
(2000).
Crystallization and preliminary X-ray analysis of a recombinant Fab fragment in complex with 17beta-oestradiol.
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Acta Crystallogr D Biol Crystallogr,
56,
1670-1672.
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W.Dall'Acqua,
and
P.Carter
(1998).
Antibody engineering.
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Curr Opin Struct Biol,
8,
443-450.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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