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PDBsum entry 1xf3
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Immune system
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PDB id
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1xf3
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References listed in PDB file
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Key reference
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Title
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Evidence for structural plasticity of heavy chain complementarity-Determining region 3 in antibody-Ssdna recognition.
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Authors
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J.P.Schuermann,
S.P.Prewitt,
C.Davies,
S.L.Deutscher,
J.J.Tanner.
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Ref.
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J Mol Biol, 2005,
347,
965-978.
[DOI no: ]
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PubMed id
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Abstract
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Anti-DNA antibodies play important roles in the pathogenesis of autoimmune
diseases. They also represent a unique and relatively unexplored class of
DNA-binding protein. Here, we present a study of conformational changes induced
by DNA binding to an anti-ssDNA Fab known as DNA-1. Three crystal structures are
reported: a complex of DNA-1 bound to dT3, and two structures of the ligand-free
Fab. One of the ligand-free structures was determined from crystals exhibiting
perfect hemihedral twinning, and the details of structure determination are
provided. Unexpectedly, five residues (H97-H100A) in the apex of heavy chain
complementarity-determining region 3 (HCDR3) are disordered in both ligand-free
structures. Ligand binding also caused a 2-4A shift of the backbone of Tyr L92
and ordering of the L92 side-chain. In contrast, these residues are highly
ordered in the Fab/dT3 complex, where Tyr H100 and Tyr H100A form intimate
stacking interactions with DNA bases, and L92 forms the 5' end of the binding
site. The structures suggest that HCDR3 is very flexible and adopts multiple
conformations in the ligand-free state. These results are discussed in terms of
induced fit and pre-existing equilibrium theories of ligand binding. Our results
allow new interpretations of existing thermodynamic and mutagenesis data in
terms of conformational entropy and the volume of conformational space
accessible to HCDR3 in the ligand-free state. In the context of autoimmune
disease, plasticity of the ligand-free antibody could provide a mechanism by
which anti-DNA antibodies bind diverse host ligands, and thereby contribute to
pathogenicity.
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Figure 2.
Figure 2. Stereo-view of the dT[3] binding site. The
protein is white; DNA is colored yellow. A s[A]-weighted mF[o]
-DF[c] electron density map is shown in blue (3s). The dT[3]
ligand and surrounding residues within 3.9 Å were omitted
prior to simulated annealing refinement and map calculation.
Shown in pink is an anomalous difference Fourier map (2.5s)
calculated from data collected using CuK[a] radiation.
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Figure 6.
Figure 6. Stereo-views of heavy chain residues 93-102 from
the two ligand-free structures, which includes HCDR3. For
reference, the sequence of heavy chain residues 93-102 is
93VRGGYRP100Y100AY100BA^100CMD^102Y. (a) HCDR3 from Fab 2 of the
P6[5] structure. (b) HCDR3 from Fab 1 of the P321 structure. The
electron density maps for both panels are simulated annealing
s[A]-weighted mF[o] -DF[c] maps and the contour level is 3s.
Prior to map calculation, heavy chain residues 94-101, along
with surrounding residues within 3.9 Å, were omitted from
the model and simulated annealing was performed. Note that
residues 98-100A (RPYY) are disordered, and they appear in the
deposited PDB entries with occupancy of zero. A theoretical
model of the backbone of residues 98-100A is drawn to help guide
the eye.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2005,
347,
965-978)
copyright 2005.
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