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PDBsum entry 2rcs
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Germline antibody
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PDB id
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2rcs
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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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Structural insights into the evolution of an antibody combining site.
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Authors
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G.J.Wedemayer,
P.A.Patten,
L.H.Wang,
P.G.Schultz,
R.C.Stevens.
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Ref.
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Science, 1997,
276,
1665-1669.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structures of a germline antibody Fab fragment and its complex with
hapten have been solved at 2.1 A resolution. These structures are compared with
the corresponding crystal structures of the affinity-matured antibody, 48G7,
which has a 30,000 times higher affinity for hapten as a result of nine
replacement somatic mutations. Significant changes in the configuration of the
combining site occur upon binding of hapten to the germline antibody, whereas
hapten binds to the mature antibody by a lock-and-key fit mechanism. The
reorganization of the combining site that was nucleated by hapten binding is
further optimized by somatic mutations that occur up to 15 from bound hapten.
These results suggest that the binding potential of the primary antibody
repertoire may be significantly expanded by the ability of germline antibodies
to adopt more than one combining-site configuration, with both antigen binding
and somatic mutation stabilizing the configuration with optimal hapten
complementarity.
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Figure 1.
Fig. 1. Ribbon superpositions of the variable regions of the
germline Fab-hapten complex (light purple) and mature Fab-hapten
complex (dark red). The aliphatic linker used to conjugate the
hapten to the carrier protein can be seen extending toward the
top of^ the figure. The side chains of the somatic mutation
sites are^ indicated in light green (germ line) and dark green
(mature) (SerL30  Asn,
SerL34 Gly,
AspL55 His,
GluH42 Lys,
GlyH55 Val,
AsnH56 Asp,
GlyH65 Asp,
AsnH76 Lys,
Ala^H78 Thr).
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Figure 2.
Fig. 2. Superposition of the structures of the germline Fab
without hapten (light blue) and the germline Fab-hapten complex
(light purple), illustrating the structural changes that occur
on hapten binding to the germline Fab. In all figures, the
aliphatic linker of the hapten has been omitted for clarity.
Gray dotted lines denote hydrogen bonds in the structure of the
germline Fab without hapten, while black dotted lines denote
hydrogen bonds in the^ germline Fab-hapten complex. (A) CDR3 of
the heavy chain is reorganized on hapten binding. To make room
for the hapten, the side chain of TyrH99 moves 6 Å away
from the hapten. The side chain of TyrH98 moves 8.3 Å and
inserts between TyrH99 and TyrH33, and TyrH33 moves toward the
phosphonate group. These movements establish a  -cation
interaction between the side chains of ArgL46 and TyrH99, a - interaction
between the aryl groups of TyrH99 and TyrH98, and a T-stack
interaction between the aryl rings of TyrH98 and TyrH33 (yellow
dotted lines). In addition, the ArgL46 side chain is stabilized
by salt bridges to the AspL55 carboxylate group and to the
TyrH99 main chain carbonyl group. (B) The interactions between
residues in CDR1, CDR2, and CDR3 of the heavy chain in the
germline^ Fab structures. The side chain of ArgH50 forms
hydrogen bonds to the hydroxyl groups of TyrH33 and TyrL94 upon
hapten binding. The guanidinium group of ArgH50 is positioned by
a hydrogen bond with AsnH56. Although TyrH33 forms one hydrogen
bond to ArgH50, it does not interact directly with either TyrL94
or the bound hapten, nor does LysH58 interact with residue H56
(cf. Fig. 3B). (C) Closeup of^ the combining site showing the
orientations of the residues directly involved in hapten binding
in the germline-hapten complex HisH35, TyrH33, and ArgL96. All
four hydrogen bonds are directed to the oxygens (red) of^ the
phosphonate group (phosphorus-yellow). TyrH33 moves 2.2 Å
toward the phosphonate group, which is a key binding determinant
in the hapten and is located in approximately the^ same position
in the combining sites of the germline and affinity-matured^
Fab-hapten complexes.
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The above figures are
reprinted
by permission from the AAAs:
Science
(1997,
276,
1665-1669)
copyright 1997.
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Secondary reference #1
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Title
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Crystal structures of the free and liganded form of an esterolytic catalytic antibody.
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Authors
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G.J.Wedemayer,
L.H.Wang,
P.A.Patten,
P.G.Schultz,
R.C.Stevens.
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Ref.
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J Mol Biol, 1997,
268,
390-400.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. Stereo views of the active site with bound
hapten. For clarity, only side-chain atoms are drawn for the
amino acid residues. Electron density is shown for the hapten
only, contoured to 2.4 σ (white lines) and 1.6 σ (blue lines).
Produced with programs O and ILLUSTRATOR.
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Figure 8.
Figure 8. Comparison of the 48G7 and 48G7-4 active sites.
This Figure shows the 2.7 Å 48G7 structure (green)
overlaid on the 2.0 Å 48G7-4 structure (blue). Backbone
atoms are almost superimposable, and only minor differences in
side-chain positions are seen. Note the rotation of the
imidazole ring for His H35. Produced with program INSIGHT II.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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The immunological evolution of catalysis.
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Authors
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P.A.Patten,
N.S.Gray,
P.L.Yang,
C.B.Marks,
G.J.Wedemayer,
J.J.Boniface,
R.C.Stevens,
P.G.Schultz.
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Ref.
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Science, 1996,
271,
1086-1091.
[DOI no: ]
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PubMed id
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Secondary reference #3
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Title
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A genetic approach to the generation of antibodies with enhanced catalytic activities.
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Authors
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S.A.Lesley,
P.A.Patten,
P.G.Schultz.
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Ref.
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Proc Natl Acad Sci U S A, 1993,
90,
1160-1165.
[DOI no: ]
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PubMed id
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